(unknown charset) Re: [AMBER] aMD plot (Daniel Roe)

From: (unknown charset) 汪盛 <shengwang.hust.edu.cn>
Date: Thu, 8 Jan 2015 08:14:47 +0800 (GMT+08:00)

Hi, Dan,
As you said last time, the following lines can be used to straight reweighting:
readdata pca12-ca
readdata amdboost
runanalysis hist pca12-ca:2 pca12-ca:3 free 300 out fhist.gnu bins 400 amd amdboost

Actually the amber manual also mentioned this option, but during the aMD process, we can get files like
(with command: $pmemd.cuda -O -i amd.in -o amd.out -p xxxxx.prmtop -c eq.rst -r amd.rst -x prod.nc):
  # Accelerated Molecular Dynamics log file
  # All energy terms stored in units of kcal/mol
  # ntwx,total_nstep,Unboosted-Potential-Energy, Unboosted-Dihedral-Energy,Total-Force-Weight,Dihedral-Force-Weight,Boost-Energy-Potential,Boost-Energy-Dihedral
        1000 1000 -44609.626477426908 792.619954823516 0.881024267543 0.300821688987 10.928587378425 17.247752481476
prod.nc:trajectory file

I think the values in amdboost can only come from amd.log. So what values are used to amdboot file: both Boost-Energy-Potential and Boost-Energy-Dihedral, or one of them.
But just like the head of file says: all energy terms stored in units of kcal/mol, so if I want to use them:
$awk 'NR%1==0' amd.log | awk '{print ($8+$7)/(0.001987*300)" " $2 "}' > amdboost

$awk 'NR%1==0' amd.log | awk '{print ($8)/(0.001987*300)" " $2 "}' > amdboost
$awk 'NR%1==0' amd.log | awk '{print ($7)/(0.001987*300)" " $2 "}' > amdboost

Is the above true? If not, how can I get the real amdboost?

Thanks a lot.

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Received on Wed Jan 07 2015 - 16:30:03 PST
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