[gmx-users] How to add DMSO as solvent?

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 6 00:09:56 CEST 2012

On 6/5/12 6:03 PM, Yun Shi wrote:
> Hello all,
> Assuming that I made my own .itp file for amber99sb-compatible DMSO parameters
> (based on Thomas Fox and Peter A. Kollman. J. Phys. Chem. B., 1998, 102,
> 8070-8079) and included that in the .top file, how can I add DMSO to my system?
> Should I also make a .gro file in analogy to spc216.gro? But how?

Create a coordinate file of a single DMSO molecule, replicate it with genconf 
-nbox, and equilibrate for a suitable length of time.  The new box of solvent 
can be used with genbox like any other.



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


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