Re: change solvent

From: Nicholas Musolino (musolino_at_mit.edu)
Date: Wed Aug 18 2010 - 12:00:57 CDT

On Aug 18, 2010, at 11:26 AM, sara wrote:
>
> Hi All
>
> if I want to solvate molecule in the other solvent ( except water) what I must to do?
>
> for example in methanol, is this change possible? and in what section I must do this changes? or anyother changes?
> Thanks
>

Since NAMD users typically employ other programs (CHARMM, Leap for Amber) to define their systems and produce .PSF (or .parm7) files, you will probably have to look into how to employ a different solvent in that software.

What are you currently doing to create these system topology files? Or what are people in your group doing?

Depending on this, I think your question might be better directed towards those programs. You could ask on CHARMM forums if you use CHARMM, for example.

Sorry there isn't a quick answer! (Although if you tLeap for AMBER topology files, it might be possible to use methanol with a single changed line in a tLeap script.)

Hope this is helpful,
Nicholas Musolino

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Nicholas Musolino
Ph.D. candidate, Department of Chemical Engineering, MIT
musolino_at_mit.edu | 617-253-6675 | Room E19-528

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