[gmx-users] Can we connect two boxes together for the simulation?

Bao Kai paeanball at gmail.com
Tue Jun 4 16:12:09 CEST 2013


I guess the renumbering of the atoms and molecules will be a problem,
especially when the two boxes contain the same type of the molecules.

How can we handle that?




editconf is a nice tool to create vacuum in your box. You can then insert
one of your box into another box using cat box1.gro box2.gro, just remove
the very last line in box1.gro.

Dr. Vitaly Chaban

On Tue, Jun 4, 2013 at 2:46 PM, Bao Kai <paeanball at gmail.com
<http://lists.gromacs.org/mailman/listinfo/gmx-users>> wrote:

>* Hi, all,*>**>* I want to do NPT simulations with different compositions first. Then I want*>* to connect the two boxes to continue the NPT simulation.*>**>* I mean, after simulations, we get two boxes with different compositions.*>**>* Can we do that with gromacs? or how can we do that?*>**>* Thanks.*>**>* Best,*>* Kai*>* --*>* gmx-users mailing list    gmx-users at gromacs.org <http://lists.gromacs.org/mailman/listinfo/gmx-users>*>* http://lists.gromacs.org/mailman/listinfo/gmx-users*>* * Please search the archive at*>* http://www.gromacs.org/Support/Mailing_Lists/Search before posting!*>* * Please don't post (un)subscribe requests to the list. Use the*>* www interface or send it to gmx-users-request at gromacs.org. <http://lists.gromacs.org/mailman/listinfo/gmx-users>*>* * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists*

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