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

Peter C. Lai pcl at uab.edu
Wed Jun 6 00:10:15 CEST 2012

There are a number of programs that will let you build coordinates of 
molecules: PRODRG, ArgusLab, VMD etc. You'll have to make sure the atom
naming and order are correct with respect to your .itp. You'll probably
have to reminimize the structure so the geometry fits the one specified 
by your FF/.itp. Then you should be able to genbox.

On 2012-06-05 03:03:28PM -0700, 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?
> Thanks for any suggestion,
> Yun

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Peter C. Lai			| University of Alabama-Birmingham
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