From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Nov 18 2010 - 19:17:03 CST
Dear Jeff,
Everything here looks ok...
the only suspicious thing that I see here is the use of periodic
temperature reassignment and Langevin dynamics at the same time, which
is not commonly done. However, this isn't the cause of the problem that
you're running into; I can do the same thing just fine in my test
simulations.
Could you please tar and send me your input and output files (including
log)? I'll see if I can reproduce the problem.
Thanks,
Peter
On 11/18/2010 01:44 PM, Jeffery Klauda wrote:
> 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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