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 - 15:30:03 PST
