PTMetad-WTE reweighting

[mandar kulkarni]

Hello everyone,

I have performed PTMetaD-WTE Belfast tutorial (GROMACS 5.0.7 + PLUMED 2.3) and trying to reweight along phi,psi using Tiwary-Parrinello reweighting scheme (J. Phys. Chem. B, 2015, 119 (3), 736–742). However, I am unable to figure out how I can combine bias from WTE (wte.bias) and metadynamic bias (metad.bias). I have attached reweighting script with the mail and it gives me the following error:

 "+++ message: assertion failed collectEnergy && energyHasBeenSet
Segmentation fault (core dumped)"

The previous discussions in the list shows this problem exists while using ENERGY CV. Please,guide me to understand how to perform correct reweighting in this case.

Also,  on the similar lines, I have another question. Let's say I am performing PTMetaD-WTE simulation with ENERGY, CV1, CV2 and Wall potential on CV3 (CV3 is not biased) , How can I combine all 3 potentials (wte.bias, metad.bias and wall.bias)

Thanks in advance.

Best Regards,
Mandar Vinod Kulkarni

[mandar kulkarni]

Hi everyone,

I have solved the confusion I had regarding combining metad.bias and wte.bias. The modifications in reweight.dat script are shown below:

PACE=1 

### Reading external bias

EXTERNAL ARG=ene FILE=BIAS_PTWTE.0.dat LABEL=wte

ener: REWEIGHT_BIAS TEMP=300.0

## During HISTOGRAM calculations LOGWEIGHTS are considered from both MeatD and Energy bias

 LOGWEIGHTS=ener,reweight

 

I am using mdrun -rerun option so that program can have energy values while reweighting.

I have another question now, regarding cluster analysis. 

Is there any possible way in plumed 2.3 so as to get reweighted trajectory to perform cluster analysis. If not, please can anyone provide guidelines or redirect me to further reading. Any help will be highly appreciated. Thanks in advance. 

[Gareth Tribello]

Hello

Well done on fixing your problem by yourself first of all.  In terms of the clustering I don’t think there are any clustering algorithms implemented within PLUMED at the moment.  I think there are some tools within gromacs that you can use. Alternatively these things are not too hard to write yourself.  If you take a look at numerical recipes in c++ you will find the algorithms that do some of these things.

I hope this helps

Gareth

-- 
You received this message because you are subscribed to the Google Groups "PLUMED users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to plumed-users...@googlegroups.com.
To post to this group, send email to plumed...@googlegroups.com.
Visit this group at https://groups.google.com/group/plumed-users.
To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/865660a0-c9fc-4d21-a143-b5302b111a86%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Mandar Kulkarni]

Thanks a lot, Gareth. I will check first how gromacs tools can help me.

On 29-Jan-2017 7:35 pm, "Gareth Tribello" <gareth....@gmail.com> wrote:

Hello

Well done on fixing your problem by yourself first of all.  In terms of the clustering I don’t think there are any clustering algorithms implemented within PLUMED at the moment.  I think there are some tools within gromacs that you can use. Alternatively these things are not too hard to write yourself.  If you take a look at numerical recipes in c++ you will find the algorithms that do some of these things.

I hope this helps

Gareth

On 29 Jan 2017, at 09:53, mandar kulkarni <mandar.kulkarni.chem@gmail.com> wrote:

Hi everyone,

I have solved the confusion I had regarding combining metad.bias and wte.bias. The modifications in reweight.dat script are shown below:

PACE=1 

### Reading external bias

EXTERNAL ARG=ene FILE=BIAS_PTWTE.0.dat LABEL=wte

ener: REWEIGHT_BIAS TEMP=300.0

## During HISTOGRAM calculations LOGWEIGHTS are considered from both MeatD and Energy bias

 LOGWEIGHTS=ener,reweight

 

I am using mdrun -rerun option so that program can have energy values while reweighting.

I have another question now, regarding cluster analysis. 

Is there any possible way in plumed 2.3 so as to get reweighted trajectory to perform cluster analysis. If not, please can anyone provide guidelines or redirect me to further reading. Any help will be highly appreciated. Thanks in advance. 

On Wednesday, 25 January 2017 22:53:23 UTC+9, mandar kulkarni wrote:

Hello everyone,

I have performed PTMetaD-WTE Belfast tutorial (GROMACS 5.0.7 + PLUMED 2.3) and trying to reweight along phi,psi using Tiwary-Parrinello reweighting scheme (J. Phys. Chem. B, 2015, 119 (3), 736–742). However, I am unable to figure out how I can combine bias from WTE (wte.bias) and metadynamic bias (metad.bias). I have attached reweighting script with the mail and it gives me the following error:

 "+++ message: assertion failed collectEnergy && energyHasBeenSet
Segmentation fault (core dumped)"

The previous discussions in the list shows this problem exists while using ENERGY CV. Please,guide me to understand how to perform correct reweighting in this case. 

Also,  on the similar lines, I have another question. Let's say I am performing PTMetaD-WTE simulation with ENERGY, CV1, CV2 and Wall potential on CV3 (CV3 is not biased) , How can I combine all 3 potentials (wte.bias, metad.bias and wall.bias)

Thanks in advance.

Best Regards,
Mandar Vinod Kulkarni 

-- 
You received this message because you are subscribed to the Google Groups "PLUMED users" group.

To unsubscribe from this group and stop receiving emails from it, send an email to plumed-users+unsubscribe@googlegroups.com.
To post to this group, send email to plumed-users@googlegroups.com.

Visit this group at https://groups.google.com/group/plumed-users.
To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/865660a0-c9fc-4d21-a143-b5302b111a86%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--
You received this message because you are subscribed to the Google Groups "PLUMED users" group.

To unsubscribe from this group and stop receiving emails from it, send an email to plumed-users+unsubscribe@googlegroups.com.

To post to this group, send email to plumed...@googlegroups.com.
Visit this group at https://groups.google.com/group/plumed-users.

To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/46B981A0-6B1E-4BA1-85BD-274989D604A8%40gmail.com.

[Massimiliano Bonomi]

You can use the g_cluster gromacs utility.
Once you get the cluster.log file with the list of clusters and cluster members,
you can calculate the unbiased cluster population by summing, for each cluster,
the weights of all cluster members obtained from the reweighting procedure (and normalize).

You could also account for the different weights in the clustering procedure itself,
but I am afraid you have to modify the g_cluster utility to read the weights.

Max

> On Jan 29, 2017, at 11:39, Mandar Kulkarni <mandar.kul...@gmail.com> wrote:
>
> Thanks a lot, Gareth. I will check first how gromacs tools can help me.
>
> On 29-Jan-2017 7:35 pm, "Gareth Tribello" <gareth....@gmail.com> wrote:
> Hello
>
> Well done on fixing your problem by yourself first of all. In terms of the clustering I don’t think there are any clustering algorithms implemented within PLUMED at the moment. I think there are some tools within gromacs that you can use. Alternatively these things are not too hard to write yourself. If you take a look at numerical recipes in c++ you will find the algorithms that do some of these things.
>
> I hope this helps
> Gareth
>

>> On 29 Jan 2017, at 09:53, mandar kulkarni <mandar.kul...@gmail.com> wrote:
>>
>> Hi everyone,
>> I have solved the confusion I had regarding combining metad.bias and wte.bias. The modifications in reweight.dat script are shown below:
>>
>> PACE=1
>>
>> ### Reading external bias
>> EXTERNAL ARG=ene FILE=BIAS_PTWTE.0.dat LABEL=wte
>> ener: REWEIGHT_BIAS TEMP=300.0
>>
>> ## During HISTOGRAM calculations LOGWEIGHTS are considered from both MeatD and Energy bias
>> LOGWEIGHTS=ener,reweight
>>
>> I am using mdrun -rerun option so that program can have energy values while reweighting.
>>
>> I have another question now, regarding cluster analysis.
>> Is there any possible way in plumed 2.3 so as to get reweighted trajectory to perform cluster analysis. If not, please can anyone provide guidelines or redirect me to further reading. Any help will be highly appreciated. Thanks in advance.
>>
>> On Wednesday, 25 January 2017 22:53:23 UTC+9, mandar kulkarni wrote:
>> Hello everyone,
>>
>> I have performed PTMetaD-WTE Belfast tutorial (GROMACS 5.0.7 + PLUMED 2.3) and trying to reweight along phi,psi using Tiwary-Parrinello reweighting scheme (J. Phys. Chem. B, 2015, 119 (3), 736–742). However, I am unable to figure out how I can combine bias from WTE (wte.bias) and metadynamic bias (metad.bias). I have attached reweighting script with the mail and it gives me the following error:
>>
>> "+++ message: assertion failed collectEnergy && energyHasBeenSet
>> Segmentation fault (core dumped)"
>>
>> The previous discussions in the list shows this problem exists while using ENERGY CV. Please,guide me to understand how to perform correct reweighting in this case.
>>
>> Also, on the similar lines, I have another question. Let's say I am performing PTMetaD-WTE simulation with ENERGY, CV1, CV2 and Wall potential on CV3 (CV3 is not biased) , How can I combine all 3 potentials (wte.bias, metad.bias and wall.bias)
>>
>> Thanks in advance.
>>
>>
>> Best Regards,
>> Mandar Vinod Kulkarni
>>
>> --
>> You received this message because you are subscribed to the Google Groups "PLUMED users" group.

>> To unsubscribe from this group and stop receiving emails from it, send an email to plumed-users...@googlegroups.com.

>> To post to this group, send email to plumed...@googlegroups.com.
>> Visit this group at https://groups.google.com/group/plumed-users.

>> To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/865660a0-c9fc-4d21-a143-b5302b111a86%40googlegroups.com.

>> For more options, visit https://groups.google.com/d/optout.
>
>
> --
> You received this message because you are subscribed to the Google Groups "PLUMED users" group.

> To unsubscribe from this group and stop receiving emails from it, send an email to plumed-users...@googlegroups.com.

> To post to this group, send email to plumed...@googlegroups.com.
> Visit this group at https://groups.google.com/group/plumed-users.
> To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/46B981A0-6B1E-4BA1-85BD-274989D604A8%40gmail.com.
>
> For more options, visit https://groups.google.com/d/optout.
>
>

> --
> You received this message because you are subscribed to the Google Groups "PLUMED users" group.

> To unsubscribe from this group and stop receiving emails from it, send an email to plumed-users...@googlegroups.com.

> To post to this group, send email to plumed...@googlegroups.com.
> Visit this group at https://groups.google.com/group/plumed-users.

> To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/CAKC_24hqfMsS0hnKFz_1b_QSi7zDgxiqZwWHj5gw5E8ShG7meg%40mail.gmail.com.

[Mandar Kulkarni]

Thanks for the detailed guideline. I will try this suggestion on alanine dipeptide case for quick understanding.

>> To unsubscribe from this group and stop receiving emails from it, send an email to plumed-users+unsubscribe@googlegroups.com.

>> To post to this group, send email to plumed...@googlegroups.com.
>> Visit this group at https://groups.google.com/group/plumed-users.
>> To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/865660a0-c9fc-4d21-a143-b5302b111a86%40googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>
>
> --
> You received this message because you are subscribed to the Google Groups "PLUMED users" group.

> To unsubscribe from this group and stop receiving emails from it, send an email to plumed-users+unsubscribe@googlegroups.com.

> To post to this group, send email to plumed...@googlegroups.com.
> Visit this group at https://groups.google.com/group/plumed-users.
> To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/46B981A0-6B1E-4BA1-85BD-274989D604A8%40gmail.com.
>
> For more options, visit https://groups.google.com/d/optout.
>
>
> --
> You received this message because you are subscribed to the Google Groups "PLUMED users" group.

> To unsubscribe from this group and stop receiving emails from it, send an email to plumed-users+unsubscribe@googlegroups.com.

> To post to this group, send email to plumed...@googlegroups.com.
> Visit this group at https://groups.google.com/group/plumed-users.

> To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/CAKC_24hqfMsS0hnKFz_1b_QSi7zDgxiqZwWHj5gw5E8ShG7meg%40mail.gmail.com.

> For more options, visit https://groups.google.com/d/optout.

--
You received this message because you are subscribed to the Google Groups "PLUMED users" group.

To unsubscribe from this group and stop receiving emails from it, send an email to plumed-users+unsubscribe@googlegroups.com.

To post to this group, send email to plumed...@googlegroups.com.
Visit this group at https://groups.google.com/group/plumed-users.

To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/D4605BDD-BED6-4A16-92B5-07A053DF97C9%40gmail.com.

[Vincenzo Maria D'Amore]

Hello Mandar and everybody,

I have performed a preliminary PT-WTE run and I am now trying to reweight my bias on the two collective variables which I am interested in using for the PT-WteMetaD simulation.

I am getting the same error...  "+++ message: assertion failed collectEnergy && energyHasBeenSet

Segmentation fault (core dumped)"

Unfortunately I didn't print my bias onto a grid during the simulation, so I only have bias written in the HILLS.0 file...

I will attach my reweight.dat file and my HILLS

Do you have any suggestion to solve the problem?

 

Thanks in advance,

Vincenzo

[Mandar Kulkarni]

Hi Vincenzo,

I used -rerun option in Gromacs mdrun to solve the error. You need energy values while reweighting, which will be calculated using -rerun option. This is mentioned in the above discussion.

Also, I think you can dump your BIAS values to the grid while rerunning by adding relevant options in PLUMED.

I hope this helps. 

Regards,

Mandar Kulkarni

--

You received this message because you are subscribed to the Google Groups "PLUMED users" group.

To unsubscribe from this group and stop receiving emails from it, send an email to plumed-users...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/862b15b0-3f1f-45ba-99fd-8482a8134e47%40googlegroups.com.

[Vincenzo Maria D'Amore]

Hi Mandar,

Thanks for your prompt reply.

I still have some questions…

Do I have to rerun the original trajectory or that processed with trjconv?

So, do I have to use the output of gromcs mdrun -rerun as input for the driver?

Ex. plumed driver --mf_trr trj.ok.trr --plumed reweight.dat --kt 2.5

To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/CAKC_24iPnJj%2BHzN46EZh%3D2TfT1xSs4PsUuK9Z4JN4zAnhs6CkQ%40mail.gmail.com.

[Mandar Kulkarni]

Hi,

Ideally, original or centered, both trajectories should give the same answers. You are using WHOLEMOLECULES. You can test the result from both trajectories for the first few frames.

Regards,

Mandar Kulkarni

To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/574FCD08-F3C1-49CD-AD05-DE092196A89B%40gmail.com.

[Vincenzo Maria D'Amore]

Hi Mandar,

Sorry for annoying you

I rerun the trajectory with the command:

-gmx mdrun -s topol.tpr -rerun trj.5.trr -plumed reweight.dat

In this way, I got the COLVAR file with the energy and with the wte.bias printed.

How can I get the fes.dat files?

To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/CAKC_24gO8i_0QKJA_LozC0zUUJF7-b8-XkjELLge93sh3y07Eg%40mail.gmail.com.

[Mandar Kulkarni]

Hi Vincenzo,

I can not point out the exact problem here. You need CALC_RCT if you are using REWEIGHT_METAD, which is absent in your reweight.dat.

You should check whether you need REWEIGHT_METAD or REWEIGHT_BIAS?

All the best,

Mandar Kulkarni

To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/E8BA62D9-F902-48DA-9C99-E240E9BEBB0B%40gmail.com.

[Vincenzo Maria D'Amore]

Dear Mandar,

I know it is difficult to fully explain the problem here but I would be grateful If you could give me more advices.

I was not able to calculate my BIAS on a grid because of the same errore you found (“looking for point out of the grid”, maybe because I didn’t use NSTCALCENERGY=1). So I am not able to CALC_RCT because it needs gris, the I am stuck in this situation, with the bias only printed on the HILLS file.

Which were your reweighing steps?

I tried to use the reweighing.dat I attached before in this way

-gmx mdrun -s topol.tpr -rerun trj.5.trr -plumed reweight.dat

But I don’t think that plumed reweighed anything, he only printed out the colvars again (which I have already printed out in first place) together with the wte bias. What I am supposed to do now?

I also tried changing “REWEIGHT_METAD” with “REWEIGHT_BIAS” but I have the same error if I don’t use mdrun -rerun and the same results if I use it.

Thank you a lot,

Vincenzo

To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/CAKC_24heQx3g5m8YfqQ%2BhgHCX_qM6peDOD%2BEBbysX6UVCki_Tg%40mail.gmail.com.