[gmx-users] shell dynamics
spoel at xray.bmc.uu.se
Sat Feb 14 10:15:02 CET 2004
On Sat, 2004-02-14 at 06:18, qiao rui wrote:
> Hi, gromacs-ers:
> I am trying to reproduce David's paper on SW water (polarizable).
> However, I am a bit confused on the procedure.
> The paper says
> 1. perform "minization of shell particle position",
> 2. a further simulation was performed using LP model.
> I am using Gromacs 3.0.5, it seems that for (1) I should use
> xmdrun, and for (2) I should use mdrun. Is this right? Also, during my
> simulation, the temperature of the system increase dramatically (>5K/1ps).
please upgrade to 3.2 first. There, mdrun and xmdrun have been merged,
and shell optimisation is done automatically if necessary.
minimzation of the shells is done at every time step. In the LP model
the shell is described as a normal particle with a small mass.
In which sim do you get large temperature increase? For SW you have to
set emtol to 0.1 kJ/mol and run in double precision.
> Has anyone here have similar experience?
> Rui Qiao
> Research Assistant
> Beckman Institute, UIUC
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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