Re: How to calculate 2d surface energy surface on segmented adaptive biased force (ABF) simulations

From: sunyeping (sunyeping_at_aliyun.com)
Date: Mon Apr 17 2017 - 21:06:19 CDT

Thank you, Jerome.
So do you mean the free energy surface should be calculated using the last ".grad" file rather than the last ".hist.grad" file?But are the ".count" and the '.hist.count" files are for the each simulation itself, not related to  its previous simulation?
Best regards.
Yeping------------------------------------------------------------------From:Jérôme Hénin <jerome.henin_at_ibpc.fr>Time:2017 Apr 18 (Tue) 04:23To:namd-l <namd-l_at_ks.uiuc.edu>; 孙业平 <sunyeping_at_aliyun.com>Subject:Re: namd-l: How to calculate 2d surface energy surface on segmented adaptive biased force (ABF) simulations
Hi,
If your ABF simulation was restarted from its previous state each time, all the information is in the last .grad file.
Best,Jerome

On 17 April 2017 at 12:54, sunyeping <sunyeping_at_aliyun.com> wrote:
Dear all, 
I wish to calculate the free energy surface determined by two reaction coordinates in ABF simulations. According to the User's Guide, it can be calculated by the abf_integrate program: 
integrate <gradient_file>My question is whether the "gradient_file" should be the ".hist.grad" file or the ".grad"?Besides, my simulation was interrupted several times and the whole simulation is composed of five successive parts. So there are five ".hist.grad" files and five the ".grad" files. So how should I use these files to calculate the free energy surface of the whole simulation?Best regards.Yeping Sun
  

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