What makes you think the linmin failures are indicative of system
instability? You should also do a quick regression test with sander to make
sure that sander and pmemd give the same results for a short number of
steps. If there's a difference, there may be something wrong (10-12
interactions are very infrequently used anymore, and are no longer part of
the standard amber force fields).
All the best,
Jason
On Tue, Oct 11, 2011 at 8:30 PM, <brian_jo.berkeley.edu> wrote:
>
>
> Hello,
>
> We compiled sander and pmemd with -DHAS_10_12 (10-12 Hydrogen Bonding
> Potential), and set up a short, 1000-step minimization run with ubiquitin.
>
> However, the HAS_10_12 flag in PMEMD creates massive instabilities and
> inaccuracies, as I compare an example output of sander and pmemd below.
> The minimization eventually terminates due to repeated LINMIN failure.
>
> We verified that the same problem occurs on multiple machines over
> multiple versions of compilers, so this problem seems to do with source
> code of PMEMD and how it treats 10-12 potential.
>
> Has anyone either encountered the same problem, or has successfully run
> PMEMD with HAS_10_12? Otherwise, a look into the PMEMD 10-12 potential
> source code would be greatly appreciated.
>
> Thank you!
>
> Brian.
>
>
> sander:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -1.8508E+04 3.9593E+02 4.3374E+04 Cl- 1235
>
> BOND = 126.0429 ANGLE = 276.9695 DIHED =
> 704.5199
> VDWAALS = 22134.3046 EEL = -45257.0072 HBOND =
> -19.4807
> 1-4 VDW = 389.3294 1-4 EEL = 3137.1801 RESTRAINT =
> 0.0000
>
>
> pmemd:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -1.8365E+04 3.9887E+02 4.3374E+04 Cl- 1235
>
> BOND = 126.0429 ANGLE = 276.9695 DIHED =
> 704.5199
> VDWAALS = 22134.3046 EEL = -45257.0072 HBOND =
> 123.1766
> 1-4 VDW = 389.3294 1-4 EEL = 3137.1801 RESTRAINT =
> 0.0000
>
> Also a segment where LINMIN failures begin accumulating in pmemd:
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 600 -5.1128E+04 7.6120E-01 5.2002E+01 O 737
>
> BOND = 5323.4082 ANGLE = 145.5072 DIHED =
> 701.6303
> VDWAALS = 8858.3346 EEL = -69553.0311 HBOND =
> -64.3119
> 1-4 VDW = 291.4799 1-4 EEL = 3038.8655 RESTRAINT =
> 130.3178
> EAMBER = -51258.1173
>
> .... RESTARTED DUE TO LINMIN FAILURE ...
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 650 -5.1350E+04 4.2329E+00 4.9058E+02 H 814
>
> BOND = 5446.7030 ANGLE = 178.9044 DIHED =
> 711.1491
> VDWAALS = 9143.3622 EEL = -70252.1102 HBOND =
> -50.7623
> 1-4 VDW = 291.3955 1-4 EEL = 3037.5668 RESTRAINT =
> 143.6471
> EAMBER = -51493.7915
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 11 2011 - 18:30:04 PDT
