Hi,
Could you give the results of the following command on our mdout file:
egrep 'NSTEP|wrapping first mol' mdout
This should output the NSTEP line as well as when it does the wrapping
to see if this happens suddenly or not.
Thanks,
Gerald.
On 04/02/2015 06:41 PM, Quynh Vo wrote:
> 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.dist3.00
> DUMPAVE=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
>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
> ____________________________________________________________________________
>
> 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
> <mailto:Gerald.Monard.univ-lorraine.fr>
> tel. : +33 (0)383.684.381
> fax : +33 (0)383.684.371
> web : http://www.monard.info <http://www.monard.info/>
>
>
> ____________________________________________________________________________
>
>
>
--
____________________________________________________________________________
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 Fri Apr 03 2015 - 05:30:02 PDT
