[gmx-users] (no subject)

[Dallas Warren]

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
again.

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
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