[AMBER] Drifting molecules despite strong restraints

From: Sanmeet Chahal <schah063.uottawa.ca>
Date: Thu, 19 Mar 2015 18:32:42 -0400

Hello all,

I am trying to run a simulation with two of the molecules being restrained
to their original positions. However after I visualize the trajectory with
VMD, the restrained molecules show a drift from their current position over

The prmtop, inpcrd, and in files can be found here:

My procedure is the following:
1) minimize, 2) heat at NPT conditions

Here are the commands I used :

sander -O -i min.in -o min-file.out -p file.prmtop -c file.inpcrd \
               -r min-file.rst -inf min-file.mdinfo -ref file.inpcrd

sander -O -i heat.in -o heat-file.out -p file.prmtop -c min-file.rst -r
heat-file.rst \
                 -x heat-file.mdcrd -inf heat-file.mdinfo -ref file.inpcrd

I have found that someone was having similar issues before:

I attempted to use the suggestion by setting nscm to be larger than nstlim
but this problem still persists.

Does anybody have an explanation for what is the cause of the drift and/or
how to solve this issue? Thank-you.

Best wishes,
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Received on Thu Mar 19 2015 - 16:00:02 PDT
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