Hi!!
I have checked all your input parameters and I don't see a mistake. Would
you mind sending me your input files (prmtop and coordinate file) that you
use when you see the problem so I can try to replicate it her and see what
is going on?
my email for the amber list is romelia.caltech.edu. You can send it
directly here if you want to keep your files private.
Best wishes,
Romelia
>
> Hello AMBER users,
>
> I am trying to run an accelerated MD simulation on a 7-residue peptide in
> explicit water (1234 waters). I have followed the protocol in the Amber-12
> manual exactly, choosing a small peptide molecule to do my first
> simulations. My input file is below (this is the sample input given on
> pages 160-161 in the Amber-12 manual, with my own parameters for EthreshD,
> alphaD, EthreshP, and alphaP).
>
> aMD dt=2.0fs with SHAKE, NPT AMD boost pot and dih
> &cntrl
> imin = 0, irest = 1, ntx = 5,
> dt=0.002, ntc=2, ntf=2, tol=0.000001, iwrap=1,
> ntb=2, cut=12.0, ntp=1, igb=0, ioutfm = 1,
> ntt = 3, temp0=310.0, gamma_ln=1.0, ig = -1,
> ntpr = 1000, ntwx = 1000, ntwr = 1000, nstlim = 2000000,
> iamd = 3, EthreshD=85,
> alphaD = 5, EthreshP = -11180,
> alphaP = 765,
> /
> &ewald
> dsum_tol=0.000001,
> /
>
> My first step was to run a normal dynamics simulation on the equilibrated
> system, and from this I calculated the aMD parameters. From this, my
> average dihedral was 60.4693, average EPtot was -11945.7808, total ATOMS
> was 3827, and protein residue number is 7.
>
> Using pmemd.MPI I have made numerous attempts to try an aMD simulation on
> this system. Each time the run stops and I get a string of error messages
> that tell me that vlimit was exceeded. Can someone tell me what this
> means? What should I be doing to correct this so the simulation will run.
> I would appreciate any suggestions that anyone might give me.
>
> Thanks!
>
> John
>
> John M. Beale, Jr., Ph.D.
> Professor of Medicinal Chemistry and Pharmacognosy
> Saint Louis College of Pharmacy
> 4588 Parkview Place
> Saint Louis, Missouri 63110-1088
> Office: 314-446-8461
> Cell: 314-315-0409
> FAX: 314-446-8460
> John.Beale.stlcop.edu<mailto:John.Beale.stlcop.edu>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
****************************************
Romelia Salomon
Walker Group
398 San Diego Supercomputing Center
UC San Diego
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Received on Thu Feb 28 2013 - 08:30:03 PST
