[AMBER] imin=5, maxcyc>1 stalls

From: Allen, Scott Edward <allense.email.unc.edu>
Date: Tue, 8 Jul 2014 13:59:59 +0000

Hello All,

I have a trajectory that contains 141 atoms (one residue- a ligand) over 5000 steps in implicit solvent that was obtained after processing REMD replicas with the script provided in Tutorial A7<http://ambermd.org/tutorials/advanced/tutorial7/>. I took the trajectories at the lowest temperature and I would like to minimize each step before doing a clustering analysis to carry the representative structures on to further steps.

When I run sander with imin=5 and maxcyc any value above 1, the calculation stalls at a point that seems to depend on the value of maxcyc that I use: when I include more minimization cycles, the calculation stalls sooner. By stalling, I mean that sander continues to run, but no more data is written and no apparent error is given, and I need to kill the program manually. I'm running AMBER on a compute cluster, but the same thing happens if I bypass the LSF submission system. If I set maxcyc=1, the calculation finishes without any problem. My full sander submission command is:

sander -O -i FrameMin.in -o FrameMin.mdout -p 133resub.prmtop -c 133resub.inpcrd -ref 133resub.inpcrd -y 133resub_remd.Ttraj.267 -e FrameMin.mden -inf FrameMin.mdinfo -x FrameMin.mdcrd

My full input file is:
imin = 5, ntx = 1, maxcyc=1000, ncyc=0, dx0=0.01,
igb = 5,
ntt = 1,
ntwx = 1,
ntwe = 1,
ntwr = 1000,
ntpr = 1,
cut = 999.0,

Any help is greatly appreciated!

Scott E. Allen, Ph.D.
Postdoctoral Associate
UNC Eshelman School of Pharmacy
Chapel Hill, NC
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Received on Tue Jul 08 2014 - 07:30:02 PDT
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