From: Jeffery Klauda (jbklauda_at_umd.edu)
Date: Thu Nov 18 2010 - 12:44:56 CST
I am trying to simulate TIP4P with another small molecule in NAMD, but
get the following error:
/FATAL ERROR: Hydrogen group error caught in rattle1()./
My input file contains, what I believe should allow for NAMD run TIP4P
(portions of the input file are shown below):
/waterModel tip4;
timestep 2.0 ;# fs/step
rigidBonds all ;# needed for 1fs steps
reassignFreq 500
reassignTemp $temperature
langevinPiston on
langevinPistonTarget 1. ;# pressure in bar
langevinPistonPeriod 50. ;# oscillation period around 100 fs
langevinPistonDecay 25. ;# oscillation decay time of 50 fs
langevinPistonTemp $temperature ;# coupled to heat bath
/
This setup works fine in CHARMM (c35b5), but when I use NAMD with the
xplor PSF the only thing I can do is minimize the energy, but
suspiciously the GPRESSURE=9999999999.9999. I believe the pdb/psf to
have the correct order (see below) for the TIP4P atoms so I am not sure
why I am getting this error. Any help would be appreciated.
PDB:
/ATOM 1 OH2 TIP4 1 -3.851 3.226 -10.107 1.00 0.00 WAT
ATOM 2 H1 TIP4 1 -3.319 2.587 -9.632 1.00 0.00 WAT
ATOM 3 H2 TIP4 1 -4.755 2.985 -9.903 1.00 0.00 WAT
ATOM 4 OM TIP4 1 -3.891 3.132 -10.035 1.00 0.00 WAT
/
PSF:
/ 1 WAT 1 TIP4 OH2 OT 0.00000
15.9994 0 0.00000 -0.301140E-02
2 WAT 1 TIP4 H1 HT 0.524220
1.00800 0 0.00000 -0.301140E-02
3 WAT 1 TIP4 H2 HT 0.524220
1.00800 0 0.00000 -0.301140E-02
4 WAT 1 TIP4 OM LP -1.04844
0.00000 -1 0.00000 -0.301140E-02
/
Thanks,
Jeff
-- ***************************************************** Jeffery B. Klauda Assistant Professor Department of Chemical and Biomolecular Engineering 2113 Building 90 University of Maryland College Park, MD 20742 Phone: (301) 405-1320 Fax: (301) 314-9126 Office: 1227A Chemical& Nuclear Engineering Bldg. Web: terpconnect.umd.edu/~jbklauda *****************************************************
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