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
equilibrate.
If you want any further information about diagnosing the current problem,
posting the .mdp file would be helpful.
-Justin
Thanks again!
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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