[AMBER] Restart file for pmemd not showing all information

From: Sasha Perkins <slperks49.gmail.com>
Date: Thu, 22 Dec 2011 11:48:17 -0500


This is one of my steps in my simulation. I noticed, however, that each
time the restart file is written during my run, there are about 80 atoms
(my system has a total of 9600 atoms) who's information is not written in
the restart file, as well as the box information is missing. However, at
the end of the run, all information is written for the last cycle. Prior
runs with the same input file but using sander showed all information in
the restart files every time the file was written.

Below is my input file which I am running using pmemd in amber 11.
 imin = 0, irest=1, ntx=5,
 ntb=2, ntp=1, taup=1.0,
 cut = 20.0,
 ntc=2, ntf=2,
 ntt=3, gamma_ln=5,
 nstlim= 400000, dt =0.002,
 ntpr=100, ntwx= 100, ntwr = 1000

Any helpful information regarding how to fix this, or if this is normal,
would be greatly appreciated since I need all information to be written in
the restart files in case my runs unexpectedly get terminated before the
maximum number of cycles is reached.

Thank you,

Sasha Perkins
Graduate Student, Penn State University
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Received on Thu Dec 22 2011 - 09:00:03 PST
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