Hi Eric,
Looking at the results you’ve shown here, it seems that your minimisation using pmemd.cuda failed. Even at step 0 of your MD, I can see you have a massive potential energy, most of which comes from the van der Waals component.
While the LINMIN FAILURE error messages are fairly common and normally innocuous (see
http://ambermd.org/Questions/linmin.html), it would be worth looking at your minimisation log, maybe logging every step, to see if there’s more going on. For example, did van der Waals close contacts actually minimise away, or are they still there even at the end of your minimisation?
I’ll also note in passing that pmemd.cuda uses not only a different algorithm, but different technology (GPU processor versus CPU), to Sander, so you shouldn’t be surprised to see numerical differences in the output, though not necessarily to this degree!
Regards,
Ben
On 22/01/2014, at 12:26 pm, Eric Smoll <ericsmoll.gmail.com> wrote:
> Hello Amber users,
>
> I am new to Amber and MD simulations in general so forgive me if I omit
> important information.
>
> I am using Amber12 on the Lonestar cluster at the University of Texas at
> Austin (
> https://www.tacc.utexas.edu/user-services/user-guides/lonestar-user-guide).
> I was able to successfully run the calculations described in the Amber
> ionic liquid tutorial (
> http://ambermd.org/tutorials/advanced/tutorial15/Tutorial2.xhtml) using
> Lonestar's installed version of sander but my attempts to run the same
> minimization and md simulations using Lonestar's installed pmemd.cuda
> program have failed.
>
> I execute the sander run with:
> sander *ARGUMENTS*
> Similary, I execute pmemd.cuda with:
> ibrun pmemd.cuda *ARGUMENTS*
>
> Comparing the the minimization mdout files for sander and pmemd.cuda, I see
> several of these lines in the pmemd.cuda mdout:
> 1283 .... RESTARTED DUE TO LINMIN FAILURE ...
> Also, the final results section reports values that are similar only in a
> crude sense (correct to 1 sigfig).
>
> Comparing the mdout files for the sander / pmemd.cuda molecular dynamics
> runs, the pmemd.cuda simulation has a massive initial energy and then it
> returns nonsense:
> 247 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 300.27 PRESS =
> 12560.4
> 248 Etot = 252311958.9026 EKtot = 3356.3765 EPtot =
> 252308602.5261
> 249 BOND = 39.0765 ANGLE = 6146.3431 DIHED =
> 94.2438
> 250 1-4 NB = 129.2998 1-4 EEL = -736.3719 VDWAALS =
> 252311026.9504
> 251 EELEC = -8097.0157 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> 252 EKCMT = 236.0287 VIRIAL = -17122.5958 VOLUME =
> 64008.0002
> 253 Density =
> 0.7330
> 254
> ------------------------------------------------------------------------------
> 255
> 256
> 257 NSTEP = 3000 TIME(PS) = 3.000 TEMP(K) =********* PRESS =
> 11252.9
> 258 Etot = ************** EKtot = ************** EPtot =
> 460713.7796
> 259 BOND = 0.0000 ANGLE = 431728.6536 DIHED =
> 5312.6252
> 260 1-4 NB = -0.0001 1-4 EEL = -1.7548 VDWAALS =
> 34273.4955
> 261 EELEC = -10599.2398 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> 262 EKCMT = 12582912.0000 VIRIAL = -5530558.9855 VOLUME =
> 74552168.2535
> 263 Density =
> 0.0006
> 264
> ------------------------------------------------------------------------------
> The sander simulation does not show this behavior.
>
> I have scanned chapter of the manual and the
> http://ambermd.org/gpus/website but I don't anything that would
> suggest that i am doing something
> wrong. I am using
> the same parameters as the tutorial. Any insights are much appreciated.
>
> Best,
> Eric
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Received on Tue Jan 21 2014 - 18:30:02 PST
