FES

[T. Salavati fard]

Dear all

I am CPMD user. I am doing metadynamics calculations and I need to reconstruct FES. I know there is a code by Teo to reconstruct free energy surface using colvar and parvar files.

My problem is finding FES program source!! I couldn't find that code to compile and try..

I appreciate your helps--Thanks

[Ari Paavo Seitsonen]

Dear T. Salavati fard,

  In <cp2k-root>/src/metadyn_tools/, if you are using the latest version? It used to be in <cp2k-root>/tools/metadyn/ earlier. One compiles by typing "make fes" in '<cp2k-root>/makefiles'.

    Greetings from Zurich,

       apsi

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[Ole Schütt]

Hi T. Salavati fard,

> One compiles by typing "make fes" in '<cp2k-root>/makefiles'.

Actually, if you are using the latest svn version you now have to type
"make graph", because the names of the make-targets now match the names
of the executables. Alternatively, you can just call make without any
targets, which will build all executables including the fes tool.


-Ole

On 2014-03-23 22:39, Ari Paavo Seitsonen wrote:
> Dear T. Salavati fard,
>
>   In <cp2k-root>/src/metadyn_tools/, if you are using the latest
> version? It used to be in <cp2k-root>/tools/metadyn/ earlier. One
> compiles by typing "make fes" in '<cp2k-root>/makefiles'.
>
>     Greetings from Zurich,
>
>        apsi
>
> 2014-03-23 21:52 GMT+01:00 T. Salavati fard
> <t.salav...@gmail.com>:
>
>> Dear all
>>
>> I am CPMD user. I am doing metadynamics calculations and I need to
>> reconstruct FES. I know there is a code by Teo to reconstruct free
>> energy surface using colvar and parvar files.
>> My problem is finding FES program source!! I couldn't find that code
>> to compile and try..
>> I appreciate your helps--Thanks
>>
>> --
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>
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>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
>   Ari Paavo Seitsonen / Ari.P.S...@iki.fi /

> http://www.iki.fi/~apsi/ [3]

>   Institut für Chemie der Universität Zürich
>   Tel: +41 44 63 55 44 97  /  Mobile: +41 79 71 90 935
>

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[Teodoro Laino]

On 24 Mar 2014, at 00:00, Ole Schütt <o...@schuett.name> wrote:

Actually, if you are using the latest svn version you now have to type "make graph", because the names of the make-targets now match the names of the executables. Alternatively, you can just call make without any targets, which will build all executables including the fes tool.

Not entirely true - using the SVN version, one can still compile FES, by typing 

> make fes

alternatively also 

> make graph

works..

Teo

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[T. Salavati fard]

Thanks all for your reply.

I've compiled fes and it seems working. But the problem is when I use it, in fes.dat all values are zero.

I've used following synatax:

fes.sopt [-cpmd] in a folder which contains colvar and parvar files.

any ideas?

Thanks in advance--

[Teodoro Laino]

fes.sopt -help

will give you an help.. Try to go though it.

You’ll have to specify -ndim and also -ndw (if I remember correctly).

Teo

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[Taha Salavati-fard]

Dear Teo,

I've tried that but still zeros!

FES|  Parsing file:   <colvar_mtd>

**********************************************************************

FES|  Parameters for FES:

FES|  NDIM         ::           2

FES|  NWD          ::           2

FES|  HILLS        ::        2156

FES|  COLVAR #   1 ::     (  2.294 , 10.688)               (   MAPPED)

FES|  COLVAR #   2 ::     (  2.278 , 10.693)               (   MAPPED)

FES|  NGRID        ::         100    100

FES|  DX           ::       0.085  0.085

FES|  CUTOFF       ::     .10000E-06

**********************************************************************

FES|  Computing Free Energy Surface

FES|  Mapping Gaussians ::  10 %

FES|  Mapping Gaussians ::  20 %

FES|  Mapping Gaussians ::  30 %

FES|  Mapping Gaussians ::  40 %

FES|  Mapping Gaussians ::  50 %

FES|  Mapping Gaussians ::  60 %

FES|  Mapping Gaussians ::  70 %

FES|  Mapping Gaussians ::  80 %

FES|  Mapping Gaussians ::  90 %

FES|  Mapping Gaussians :: 100 %

FES|  Dumping FES structure in file: < fes.dat >

FES| NORMAL FES TERMINATION.

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[Teodoro Laino]

can you post your files?

[Taha Salavati-fard]

Yes of course,

Here they are!

[Teodoro Laino]

On my laptop, when I run:

fes.sopt -cpmd -ndim 2

I get the fes.dat file attached. Which is everything but not zero.

Can you please attach your fes.dat output file generated by fes.sopt ?

Teo

[Taha Salavati-fard]

Thanks Teo.

Problem might be due to old linux on the cluster I am using. I am going to try it again on my laptop and will let you know.

Thanks for great helps.

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<colvar_mtd><parvar_mtd>

[Teodoro Laino]

please, post that file.

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<colvar_mtd><parvar_mtd>

[Taha Salavati-fard]

here it is

[Teodoro Laino]

mmm… strange..  it could really be some issue with the compiler..

Teo

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<fes.dat>

[Taha Salavati-fard]

I'll try with different compiler and let you know.

thanks--

[Taha Salavati-fard]

Dear Teo,

I've compiled it again on different machine with latest ubuntu.

fes.dat this time contains zeros and NaNs !!

I used exactly same files that I have sent to you!

[Teodoro Laino]

which compiler ?

[Taha Salavati-fard]

I guess it is gfortran