[AMBER] MASK with distance in AMBER.

From: Parviz Seifpanahi Shabane <sparviz.vt.edu>
Date: Fri, 12 Aug 2016 11:48:32 -0400

Hi All,
I need to use the mask command with distance for my job (below). as you
know for using the mask with the distance we need to give the reference to
Cpptraj. I need to know, how to Cpptraj work on this situation?
 My impression is that Cpptraj uses the reference for finding the molecules
(in my case water) in the special distance which was defined by the mask
from the reference file and then track those molecules down during the
simulation, is that correct?(number of molecules did not change for my
does the Cpptraj update the molecules for each frame?
it could be the bug for Cpptraj because molecules will move during the
simulation and too many of properties (in my case auto-correlation function
of the dipole of water molecules near the protein) depend on the position
of molecules.

parm 3v03-H++-2braanch.top
reference 3v03-H++-2braanch.prod1.restrt
trajin 3v03-H++-2braanch.prod2.traj

mask (:1-1158<:6.0)&:WAT
vector v0 dipole out dipole-G6A.dat (:1-1158<:6.0)&:WAT
timecorr vec1 v0 out auto-correlation-function-G6A.dat order 1

Best Regards
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Received on Fri Aug 12 2016 - 09:00:02 PDT
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