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

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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