Dear amber users,
Sorry for that I can't reply to my previous email as I subscribe to the maillist in the wrong way. I recently tried to use Amber18 and 16 pmemd.cuda to run triplicated jobs, but I got exactly the same trajectory for all three trials(final coordinate file and output (energy, temperature, etc.) files are same ) with a different random seed for Amber18 and also get several same trajectories by using Amber16. I'm not sure if there any problems with the random seed or the installation on the cluster is wrong.
==============minimization input file================
&cntrl
imin=1, maxcyc=2000, ncyc=250, drms=0.05,
ntb=1, ntf=1, ntc=1,
cut=12.0,
ntr=1,
restraintmask="(!:WAT)&(!.H=)&(!.Na+)|(!.Cl-)",
restraint_wt=5.0,
ntpr=50
ioutfm=1,
/
================================================
Any reply will be very grateful. Thank you!
With regards,
Jinfeng
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Received on Tue Sep 17 2019 - 07:00:02 PDT
