Re: [AMBER-Developers] [AMBER] manual prmtop file editing for free energy calculation

From: Ross Walker <ross.rosswalker.co.uk>
Date: Sun, 27 May 2012 18:36:58 -0700

> > This also means, incidentally, that the OPLS force field is not
> properly
> > supported by pmemd.cuda since the original NB coefficients are
> > de-combined and re-combined using the Amber combining rules. This was
> a
> > relatively recent discovery of ours which I haven't gotten a chance
> to
> > really pursue.
>
> It also means that NBFIX will not work correctly, i.e. CHARMM ion
> parameters, etc. People could convert over PSF's and not get the same
> results when running on GPUs. I notice now that the DHFR test case in
> test/chamber/md_engine gives slightly different VDW with pmemd.cuda vs.
> pmemd or sander... --tom


$AMBERHOME/test/cuda/chamber/dhfr_cmap_pbc/

CPU 
---
 NSTEP =        0   TIME(PS) =       0.000  TEMP(K) =   445.01  PRESS =
0.0
 Etot   =   -185298.7667  EKtot   =     50131.6843  EPtot      =
-235430.4510
 BOND   =       139.2187  ANGLE   =      5018.3206  DIHED      =
740.9486
 UB     =        29.6490  IMP     =        14.2418  CMAP       =
-216.2392
 1-4 NB =       345.7376  1-4 EEL =      6475.6373  VDWAALS    =
29478.9185
 EELEC  =   -277456.8839  EHBOND  =         0.0000  RESTRAINT  =
0.0000
 Ewald error estimate:   0.3557E-04
GPU_DPDP
--------
 NSTEP =        0   TIME(PS) =       0.000  TEMP(K) =   445.01  PRESS =
0.0
 Etot   =   -185298.7667  EKtot   =     50131.6843  EPtot      =
-235430.4510
 BOND   =       139.2187  ANGLE   =      5018.3206  DIHED      =
740.9486
 UB     =        29.6490  IMP     =        14.2418  CMAP       =
-216.2392
 1-4 NB =       345.7376  1-4 EEL =      6475.6373  VDWAALS    =
29478.9185
 EELEC  =   -277456.8839  EHBOND  =         0.0000  RESTRAINT  =
0.0000
Looks absolutely identical to me... What's the issue?
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
|             Assistant Research Professor              |
|            San Diego Supercomputer Center             |
|             Adjunct Assistant Professor               |
|         Dept. of Chemistry and Biochemistry           |
|          University of California San Diego           |
|                     NVIDIA Fellow                     |
| http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk  | 
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Received on Sun May 27 2012 - 19:00:03 PDT
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