[gmx-users] (no subject)

James Krieger jamesmkrieger at gmail.com
Mon Jul 16 04:26:15 CEST 2018

You can probably use gmx solvate for this with the frame at the end of 50
ns as input cp and a box of the new molecules as cs or possibly genion. We
also have a tool for building simulation systems with small molecules
called DruGUI http://prody.csb.pitt.edu/drugui/ although I don't know how
you would convert the topology from NAMD .psf to Gromacs .top format.

Best wishes

On Tue, Jul 10, 2018 at 7:21 AM, Soham Sarkar <soham9038 at gmail.com> wrote:

> Dear all,
>  I am planning to do a simulation where after 50ns of simulation I want to
> add some other chemicals in the system and continue it for another 50ns, so
> that I can have the effect of that chemicals exclusively before and after
> adding it to the system.Is it at all possible? If yes please tell me the
> protocol/ commands or give me some references where this type of simulation
> is used. Thanks in advance.
> -Soham
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