[gmx-users] Chloroform (CHCl3) solvent box for G53a5 force field

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 20 17:51:10 CEST 2009

Pablo Englebienne wrote:
> Hi all,
> 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!


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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