I had just hit a vlimit (velocity limit) issue with a non-AMD simulation I was working on.
For my work, an otherwise ligand held in place via an NMR restraint to molecule 1 was imaged to an adjoing cell, so on restart, there was 70,000 kCal of energy where there had only been 10 kCal in the closing restart file of the prior run.
This resulted in tremendous velocity being transferred to the restrained ligand - and the vlimit was absolutely exceeded.
I have not had this problem with an AMD run (yet). Mathematically, amd adds to the force calculations in a quite simple way, so I would be surprised to find AMD specifically to be at the root of the problem. Review the energetics of the coordinates under simulation first. Are there any high energy terms?
If I were debugging this from computer-scientist perspective, I would dial down the boosting potentials so that there is in essence "no boost" - and review my settings of those parameters extra-carefully. Are temperature controls being performed in a manner consistent with the recommendations of the AMD community?
________________________________________
From: Beale, John [John.Beale.stlcop.edu]
Sent: Thursday, February 28, 2013 7:27 AM
To: amber.ambermd.org
Subject: [AMBER] aMD
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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Received on Thu Feb 28 2013 - 08:30:04 PST
