[gmx-users] shell dynamics
spoel at xray.bmc.uu.se
Sat Feb 14 21:09:01 CET 2004
On Sat, 2004-02-14 at 20:49, qiao rui wrote:
> Thanks David for the quick reply.
> The temperature increase is observed during the first few pico second, and
> after that it is normal (I did not run it too long yesterday).
> I installed version 3.2, but this time grompp pops a new error:
> "Water polarization should now be listed under [ water_polarization ]".
> I am assuming that the .itp file for the SW model has some problem. How do
> I modify the .itp file?
take the one from share/top
> I have two addition questions:
> 1. if I have other molecules in the system, should the shell atom interact
> with them?
this is your choice, there is AFAIK one person combining this potential
with ions, we haven't done that.
> 2. To my impression, one first need to equilibrate system using shell
> minimization for a while (say, 50ps, using time step 1fs), and then one
> can switch to LP model (using time step 0.2 fs). To switch to LP model,
> can I simply increase the emtol to 100 so that no optimization is done?
LP model is bad. Don't use it. It has nothing to with SW, but in the
paper we used it to have something to compare to. Now there is also the
MCDHO model (StMartin et al.) but it doesn't work in standard gromacs.
> by the way, the simulation is kind of slow for even a small system (900
> water molecules -> 200 hours/1ns), is this normal?
Depends on your CPU of course, but it seems like a lot. Maybe it's a bit
better when you use emtol = 1.
> Thanks for your help!
> 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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