[gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field
Justin A. Lemkul
jalemkul at vt.edu
Wed Oct 21 01:18:05 CEST 2009
Pablo Englebienne wrote:
> Thanks for confirming this, Justin.
> I decided not to use the user-contributed CHCl3 box because the topology
> is not consistent with the GROMOS atom types: the CH is united atom
> (although the mass is 12.01100, it should probably be 13.01900?), while
> in G53a5 there are parameters for C, H and Cl. Has someone ever used
> this box successfully?
> I was able to equilibrate the box in NVT (100-200ps gives a stable
> simulation), although it exploded at constant pressure. After looking at
> some references on the mailing lists (both GMX and AMBER), I tried
> increasing tau_p from 2.0 to 5.0 and that yielded a stable 100 ps
> simulation, although the system later (continuing for further ~150 ps)
> started to oscillate wildly in temperature and pressure.
> What is the effect of increasing tau_p? Besides making the dynamics
> stable, would changing its value affect the outcome of the simulation in
> any other way?
By increasing tau_p you are reducing the stringency of the pressure coupling,
i.e. allowing the system to change a bit more between coordinate scaling. By
decreasing the frequency of coordinate scaling in extremis, you would lose the
benefit of pressure coupling and achieve an NVT ensemble, with the box
dimensions being essentially static. In the case of a tau_p of 2.0 vs. 5.0, you
should not have this problem.
If the provided box uses a united-atom CH, I would suspect it is not suitable
for GROMOS96 parameters, as you have discovered. In all G96 variants, the H is
explicitly represented. You might consider coming up with your own box. Start
with a coordinate file for one molecule, use genconf to generate a box, and
If you want any further information about diagnosing the current problem,
posting the .mdp file would be helpful.
> Thanks again!
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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