Hi all,
It seems that I have the same kind of problem than Fabricio Bracht (last
week on the mailing list) with the cuda version of pmemd.
Basically, I'm using pmemd.cuda_SPFP to simulate a protein with various
ligands. My setup is always
the same, and I run 1 simulation per different ligand. For one ligand, I
obtain the following error:
cudaMemcpy GpuBuffer::Download failed unspecified launch failure
I have run 5 times 100 ns without any problem (5 different sets of
ligands). And this 6th simulation fails.
For information, I recompiled pmemd.cuda with the latest updates and the
problem still exists (no difference between SPDP and SDFP versions for
example). I use intel 12.1.3 and cuda 4.2. The GPU card is a Tesla M2090.
From some analysis of the mdcrd file, it seems that a SHAKE problem
occurs on the ligand: at some point, the distance between a nitrogen and
its bonded hydrogen becomes 5 angstroms!
I'm currently re-running with a smaller time step to see if it can
correct anything (1fs instead of 2fs).
Any idea on how to correct the problem?
Thanks in advance,
Gerald Monard.
For the record, the mdin file is:
&cntrl
imin = 0, ntx = 5, irest = 1,
dt = 0.002, nstlim = 500000,
ntb = 1, ntp = 0,
ntt = 1, temp0 = 10., tempi = 10., vrand = 100,
ntc = 2, ntf = 2,
iwrap = 1,
ntpr = 100, ntwx = 1000, ntwv = 1000, ntwe = 1000,
ntr = 0,
nmropt = 1,
/
&wt
TYPE=TEMP0,
ISTEP1 = 1, ISTEP2 = 500000,
VALUE1 = 10.0, VALUE2 = 150.0,
/
&wt
TYPE=END
/
An excerpt of the mdout file is:
NSTEP = 495000 TIME(PS) = 1390.000 TEMP(K) = 159.27 PRESS
= 0.0
Etot = -469049.8444 EKtot = 44215.6094 EPtot =
-513265.4538
BOND = 2046.4235 ANGLE = 6216.2352 DIHED =
11831.1310
1-4 NB = 3996.5630 1-4 EEL = 51903.4316 VDWAALS =
89945.5259
EELEC = -679204.7641 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 495100 TIME(PS) = 1390.200 TEMP(K) = NaN PRESS
= 0.0
Etot = NaN EKtot = NaN EPtot =
**************
BOND = 0.0000 ANGLE = 2313881.3573 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
**************
EELEC = ************** EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
--
____________________________________________________________________________
Prof. Gerald MONARD
Theoretical Chemistry and Biochemistry Group
SRSMC, Université de Lorraine, CNRS
Boulevard des Aiguillettes B.P. 70239
F-54506 Vandoeuvre-les-Nancy, FRANCE
e-mail : Gerald.Monard.univ-lorraine.fr
tel. : +33 (0)383.684.381
fax : +33 (0)383.684.371
web : http://www.monard.info
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Received on Thu Sep 27 2012 - 15:00:03 PDT
