Re: Reg : MD simulation with DMSO instead of water

From: Axel Kohlmeyer (
Date: Tue Jun 17 2014 - 06:12:55 CDT

On Tue, Jun 17, 2014 at 1:04 PM, Akshay Bhatnagar
<> wrote:
> Can anyone please tell how can i solvate an amino acid in DMSO instead of
> water. Like from where i can get the parameter, topology, pdb and psf files
> for DMSO?

like with any other (custom) molecule: from the published literature
and with a text and/or molecule editor program

furthermore, you will likely also need to reparameterize the amino
acid, since the typical parameters are tuned for a specific(!) water
model. if people already criticize the change of water potentials as
inconsistent, you can easily imagine what the attitude towards
changing to a completely different solvent is going to be.


> Thank you
> With Regards
> Akshay Bhatnagar
> PhD Student
> BITS Pilani Hyderabad Campus

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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