Re: [AMBER] Distance based energy calculation

From: Daniel Roe <>
Date: Thu, 20 Sep 2018 11:13:41 -0400


On Thu, Sep 13, 2018 at 9:46 AM MOHD HOMAIDUR RAHMAN
<> wrote:
> 1) how to assign reference so that it will update with each frame of
> trajectory?
> 2) For energy calculation the assign mask for water-water is correct.

You can't directly. Distance-based masks for actions are determined
using the active reference frame (default first reference loaded).
This is because the number of atoms selected with a distance-based
mask can vary, which would require that Actions be set up for every
frame, which is currently not done. However, I think a better approach
for selecting the first solvation shell would be to first run
'watershell' to get an estimate for how many waters are in the first
shell on average, then use the 'closest' command to keep this number
of waters. This way the number of atoms will be consistent. The
'unstrip' command can be used to revert the effects of 'closest' so
you can do multiple passes in the same run. You can even use simple
data set math to get your deltaE. For example, say you ran
'watershell' and determine that on average there are 119 waters in the
first shell:

parm traj.parm7
closest 119 !:WAT
energy Protein_Water etype simple nb14 nonbond elec vdw
strip :WAT
energy Protein_Protein etype simple nb14 nonbond elec vdw
closest 119 !:WAT
strip !:WAT
energy Water_Water etype simple nb14 nonbond elec vdw
delta = Protein_Water[total] - Protein_Protein[total] - Water_Water[total]
writedata ene.dat *[total] delta

Hope this helps.


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Received on Thu Sep 20 2018 - 08:30:03 PDT
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