I'm trying to simulate a small molecule in a chloroform box using the
GROMOS G53a5 forcefield. I realized that the parameters for the
solvent
are present in the ffG53a5.rtp file, however I could not find a CHCl3
solvent box included in GROMACS. I did find, however, a CHCl3 solvent
box equilibrated by PeiQuan Chen
(http://lists.gromacs.org/pipermail/gmx-users/2003-May/005572.html)
at
http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies
.
I also saw mention of a box for the Amber forcefield, that is now
included in AmberTools (amber10/dat/solvents/cform/cform.pdb and
chcl3_equil.pdb.1). I took this one and I'm equilibrating it to use
it
later.
In the mean time, I wanted to know if I overlooked something, and
there
is a CHCl3 box to use with the GROMOS forcefield?
Not one that is officially distributed. If it was, it would be the
/share/gromacs/top subdirectory with other solvent topologies and
structures.
Probably your best bet is to use the one in the User Contributions
section,
unless you feel the need to create your own and start from scratch.
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?
Thanks again!
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