free energy profile calculation

Jie Zhong dynami... at gmail.com
Wed Nov 16 16:39:23 CET 2016


Hi Marcella,

Thanks for your information.
I try to plot the FES with the sub-program that is compiled with cp2k. 
However, I got the following error. 
fes.sopt -cp2k -ndim 1 -ndw 1 -file bulk-HNCO-1.restart

**********************************************************************
FES|  Parsing file:   <bulk-HNCO-1.restart>

At line 185 of file 
/opt/programs/cp2k-2.4.0/makefiles/../tools/metadyn/graph_utils.F
Fortran runtime error: Bad real number in item 1 of list input.

Did you use the sub-program in cp2k to calculate FES before? Any suggestion 
for my error would be appreciated.

Best
Jie


在 2016年11月12日星期六 UTC-6上午5:11:16,Marcella Iannuzzi写道:
>
> Hi Jie,
>
> Indeed in the restart file all required information to build the free 
> energy hyper surface are stored, i.e, positions, widths and heights of the 
> hills. To sum up the Gaussians you can use the tool that you prefer.
> As previously suggested the tool provided with plumed would be a solution.
> Another possibility would be the sub-program graph that is compiled 
> together with cp2k.
>
> Kind regards
> Marcella
>
> On Tuesday, November 8, 2016 at 4:46:55 PM UTC+1, Jie Zhong wrote:
>>
>> Hi all,
>>
>> I am trying to get familiar with cp2k metadynamics method. I have 
>> finished the calculation.
>> I was told to use the restart file to plot free energy profile as 
>> function of collective variable. How can I do it?
>> The restart file has been attached.
>> Any suggestion is appreciated.
>>
>> Best
>> Jie
>>
>>
>>
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