Hi Brian,
What version of Amber? What compile flags for pmemd? There is code in place through Amber 10 for sure, though it was rarely tested, so a bug is not completely out of the question. I don't know just yet what the status in Amber 11 is, whether there may be GPU support issues, etc.
Regards - Bob Duke
________________________________________
From: brian_jo.berkeley.edu [brian_jo.berkeley.edu]
Sent: Tuesday, October 11, 2011 5:30 PM
To: amber.ambermd.org
Subject: [AMBER] Question regarding HAS_10_12 flag in PMEMD (LINMIN Failure)
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
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Received on Tue Oct 11 2011 - 18:00:04 PDT
