Step at which use of coarse grained trajectory in IBI starts

[Pragati Sharma]

Dear all,

I am simulating a polymer using IBI. I have a confusion, at what step is the coarse grained trajectory is generated and used.

The process I am following is:

1.csg_mapp : To generate out.gro using mapp.xml

2. csg_stat : To generate distributions, but it also uses the atomistic trajectory traj_comp.xtc

csg_stat --top topol.tpr --trj traj_comp.xtc --cg mapp_5mer.xml  --options settings.xml

3. csg_boltzmann : To generate potentials, but it also uses the atomistic trajectory traj_comp.xtc

csg_boltzmann --top topol.tpr --trj traj_comp.xtc --cg mapp_5mer.xml  < boltzmann_cmds

4. csg_call: To smoothen the potentials

5. csg_inverse:

csg_inverse --options settings.xml 

Excerpts from Settings.xml:

<map>buta_cg.xml</map>

   <!-- these files are copied for each new run -->

   <filelist>grompp.mdp topol.top table.xvg index.ndx</filelist>

   <!-- do so many iterations -->

   <iterations_max>50</iterations_max>

 

I think in this 5th step only, a CG trajectory is generated and used. 

Am I correct with the steps. 

Also, are the distributions generated from csg_stat are the target ones that are to be compared with the ones obtained from last step of csg_inverse.

Thanks

Pragati

[Christoph Junghans]

Yes, that is both correct, csg_inverse will generate the CG trajectory in each step and compare its distributions to the target ones that you generated with cag_stat in step 2.

Christoph 

Thanks

Pragati

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Christoph Junghans
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[Pragati Sharma]

Thanks Christoph for the clarification.

 

I have one more point to understand.

I have read in some paper that, the IBI process is started from bond and then angle, then the nonbonded potential is finished at last. When doing ibi for bond and angle, the pair interaction is turned off. How is this turning off done.

While trying to do sequentially, If I want to do IBI of a bond type, say A-B first. Do I still be needing tabulated potentials for angle or non-bonded types using csg_inverse.

I generated a table_b0.xvg file for A-B bond using commands csg_boltzman and csg_call and put it in main directory and then I run csg_inverse.

But my simulation stops at step_001 asking for other table_b1.xvg (other bond) and table_a1.xvg (other angle) files.

The error is:

"Tabulated interaction of type 'Tab. Angles' with index 0 cannot be used

because no table file whose name matched '_a0.xvg' was passed via the gmx

mdrun -tableb command-line option"

Also while taking all interactions at once in settings.xml, simulation stops at step_001 stating:

"Fatal error:

A tabulated bond interaction table number 1 is out of the table range: r

2.030714, between table indices 1015 and 1016, table length 1001"

I want to know, how I can optimize bond, angle, dihedral and then non-bonded potentials one by one and run IBI simulation.

I am attaching the settings.xml file that I used for getting A-B potential only using csg_inverse and the table_b0.xvg file for AB bonded interaction.

Thanks,

Pragati

[Christoph Junghans]

On Tue, Jul 21, 2020 at 5:01 AM Pragati Sharma <praga...@gmail.com> wrote:
>
> Thanks Christoph for the clarification.
>
> I have one more point to understand.
> I have read in some paper that, the IBI process is started from bond and then angle, then the nonbonded potential is finished at last. When doing ibi for bond and angle, the pair interaction is turned off. How is this turning off done.
>
> While trying to do sequentially, If I want to do IBI of a bond type, say A-B first. Do I still be needing tabulated potentials for angle or non-bonded types using csg_inverse.

Yes, you still need to provide a table for the bonded interactions
even if you are doing ibi for the non-bonded interactions only (unless
you are using functional forms for the bonded tables of course).

>
> I generated a table_b0.xvg file for A-B bond using commands csg_boltzman and csg_call and put it in main directory and then I run csg_inverse.
> But my simulation stops at step_001 asking for other table_b1.xvg (other bond) and table_a1.xvg (other angle) files.
>
> The error is:
>
> "Tabulated interaction of type 'Tab. Angles' with index 0 cannot be used
> because no table file whose name matched '_a0.xvg' was passed via the gmx
> mdrun -tableb command-line option"

You might have forgotten to add the table to the filelist, so that
they get copied for to each iterations step.
VOTCA will automatically add the table to the gmx command line, but
you can also do it manually in cg.inverse.gromacs.mdrun.opts

>
>
> Also while taking all interactions at once in settings.xml, simulation stops at step_001 stating:
>
> "Fatal error:
> A tabulated bond interaction table number 1 is out of the table range: r
> 2.030714, between table indices 1015 and 1016, table length 1001"

This usually means the bond got stretched too far. You either need to
make the table longer or the interaction more repulsive towards the
end.

Also have a look at:
https://github.com/votca/csg-tutorials/tree/master/hexane
the ibi_all / ibi_nonbonded examples covers the case where of IBI for
all interactoins vs IBI for only non-bonded interactions.

Christoph

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