Re: [AMBER] error **** in output file with wrapping first molecule on GPU

From: Quynh Vo <ziczac_nq.yahoo.com>
Date: Thu, 2 Apr 2015 16:41:23 +0000 (UTC)

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
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Received on Thu Apr 02 2015 - 10:00:03 PDT
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