Date: Thu, 28 Feb 2013 07:27:17 -0600
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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