Hi, thank you for your help. Yes I noticed those huge numbers too and I can't really understand how or why!! I used wrapping for both heat and production. I used ntb = 2 during heating to get the right density and volume. And this error did not occur using pmemd.MPI, only with pmemd.cuda
My input file:
&cntrl imin = 0, ntx = 5, irest = 1, iwrap = 1, ig = -1, tol = 0.000001, ntb = 1, cut = 10, ntt = 3, ntc = 2, ntf = 2, tempi = 298.15, temp0 = 298.15, gamma_ln = 5.0, ntp = 0, pres0 = 1.0, taup = 2.00, nstlim = 2000000, nscm = 1000, dt = 0.001, ntpr = 20000, ntwx = 20000, ntwr = 200000, nmropt=1,
/ &wt type='DUMPFREQ', istep1=1000, / &wt type='END' /DISANG=rst.dist3.00DUMPAVE=dist_3.00.dat Best regards,
Quynh Vo
On Thursday, April 2, 2015 12:13 AM, Gerald Monard <Gerald.Monard.univ-lorraine.fr> wrote:
Hi,
The 3 numbers after "wrapping first mol" are the translation vector
components that are used to move your atoms back into the box. These
numbers are _huge_.
Is it the first time that the wrapping is used? (check your mdout output
and the vector components)
What's the value of your input (mdin) file?
Did you apply ntb != 0 when you heated your system?
Finally, does this error also occur when using pmemd.MPI (without CUDA)
Gerald.
On 04/02/2015 08:00 AM, Quynh Vo wrote:
> Dear Amber users,
> I've been having this problem using GPU code of Amber12 to perform Umbrella sampling study. Whenever "wrapping first molecule" appeared in mdout file, several values become ***** (see below). If I let it, the simulations would come to completion. I ran these simulations on several GPUs (tesla M2090, GTX 560, 570, 580, 650Ti, 660, 680, 780) and the problem occurred on all of them. Before finding this thread (http://archive.ambermd.org/201202/0426.html), I tried running the system both with and without iwrap but that didn't help. The system was heated slowly with ntt=3 and production runs were performed using NVT ensemble with irest = 1 and ntx = 5. I couldn't find any additional information after that thread in 2012. Is it still a bug of GPU code? Or does it have something to do with my system?
> Thank you for your help.
> NSTEP = 1300000 TIME(PS) = 2300.000 TEMP(K) = 298.11 PRESS = 0.0 Etot = 13796.4843 EKtot = 8434.3867 EPtot = 5362.0976 BOND = 1117.6359 ANGLE = 5675.9479 DIHED = 2508.6295 1-4 NB = 717.9007 1-4 EEL = -476.9713 VDWAALS = -4782.1699 EELEC = 585.1969 EHBOND = 0.0000 RESTRAINT = 15.9278 EAMBER (non-restraint) = 5346.1698 ------------------------------------------------------------------------------
> NMR restraints: Bond = 0.442 Angle = 0.000 Torsion = 2.171===============================================================================wrapping first mol.: -64156.49584 -490243.09177 317751.07235
> NSTEP = 1320000 TIME(PS) = 2320.000 TEMP(K) =********* PRESS = 0.0 Etot = ************** EKtot = ************** EPtot = ************** BOND = -0.0000 ANGLE = 798521.7102 DIHED = 6235.9991 1-4 NB = 0.0000 1-4 EEL = 0.0008 VDWAALS = 894384357.7648 EELEC = -302.2937 EHBOND = 0.0000 RESTRAINT = ************** EAMBER (non-restraint) = 895188813.1812 ------------------------------------------------------------------------------ Best regards,
> Quynh Vo
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--
____________________________________________________________________________
Prof. Gerald MONARD
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 Apr 02 2015 - 10:00:03 PDT
