Hi,
aMD experts may want to chime in, but yes I think to get the total
boost for iamd=3 you just sum up the dihedral and potential boosts
(and of course convert to KT by dividing by kB*temperature, as you are
doing).
-Dan
On Wed, Jan 7, 2015 at 5:14 PM, 汪盛 <shengwang.hust.edu.cn> wrote:
> 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):
> amd.log:
> # 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
> evecs-ca.dat:
> pca12-ca:
> 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
>
> or
> $awk 'NR%1==0' amd.log | awk '{print ($8)/(0.001987*300)" " $2 "}' > amdboost
> or
> $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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jan 08 2015 - 07:30:06 PST
