[gmx-users] (no subject)

Dallas Warren dallas.warren at monash.edu
Wed Jul 11 06:30:48 CEST 2018

If you aren't adding anything too big, or to much of them, then take
the final frame, use gmx insert-molecules (probably with a reduced vdw
radius so they fit in) to put the additional molecule(s) in, perform
standard pre production run energy minimisation etc, then off it goes

Why can't you start two separate systems, one without, and one with?
That would be a more robust way to do it.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Tue, 10 Jul 2018 at 21:22, 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
> --
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list