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:
&cntrl
imin = 5, ntx = 1, maxcyc=1000, ncyc=0, dx0=0.01,
igb = 5,
ntt = 1,
tol=0.00001,
ntb=0,
ntc=1,
ntf=1,
ntwx = 1,
ntwe = 1,
ntwr = 1000,
ntpr = 1,
cut = 999.0,
itgtmd=1,
tgtrmsd=0.0,
tgtmdfrc=0.000,
tgtfitmask=".1,3,79,83,84,86",
tgtrmsmask=".1,2,32,33,34,19,20,21,42,43,44,5,6,7,49,50,51,13,14,15,57,58,59,71,72,73,77,78,79",
/
Any help is greatly appreciated!
-Scott
--
Scott E. Allen, Ph.D.
Postdoctoral Associate
UNC Eshelman School of Pharmacy
Chapel Hill, NC
scottallenphd.gmail.com<mailto:scottallenphd.gmail.com>
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Received on Tue Jul 08 2014 - 07:30:02 PDT
