[gmx-users] gmx insert-molecule issue- not getting the number atoms inserted wanted

Mark Abraham mark.j.abraham at gmail.com
Thu Feb 15 20:26:19 CET 2018


There's not enough information to say. What makes you think your molecules
will fit in the spaces you say are there? What radii did you suggest for
the atoms in your molecules?


On Thu, Feb 15, 2018 at 6:54 PM Joydeep Munshi <jom317 at lehigh.edu> wrote:

> Hello,
> I have a system of polymer(P3HT)-fullerene system. I am using initially
> Insert-molecule command to insert N number of P3HT molecules followed by
> PCBM molecules. Finally I am solvating the system using Solvate command.
> While I am trying to insert N=300 atoms it is successfully inserting all of
> them. However, while I am inserting more than 350 molecules, it is failing
> to do that. I tried to increase -try flag to 25000-30000 so that it can
> insert. But I am failing to do that.
> However my box does have empty volume after inserting, say 350 P3HT
> molecules, when it is failing to insert more. Is there any way to get this
> done efficiently to insert more atoms to the system?
> Is there any option to insert molecules using parallel processing.
> Thanks in advance.
> *Thanks and regards,*
> *Joydeep Munshi,*
> *Graduate Research Assistant,*
> *Packard Lab 375,*
> *Mechanical Engineering and Mechanics,*
> *Lehigh University*
> *Contact: (484)-821-6702*
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