[gmx-users] How to get the complete molecule?
Victor Rosas Garcia
rosas.victor at gmail.com
Sat Jul 7 20:59:45 CEST 2018
try "-pbc whole" instead of "-pbc mol"
El sáb., 7 jul. 2018 a las 2:13, Anjana Jayasinghe (<anjusilva90 at yahoo.com>)
> Dear All,
> In my simulation, part of my molecule is in a one cell and the other part
> is in the adjacent cell. I want to get the complete molecule in the pdb
> format in the center of the box. I tried to do that using gmx trjconv -f
> run.pdb -s run.tpr -pbc mol -ur compact -center -o run_new.pdbBut I
> couldn't get what I want. Can anyone help me?
> Thank you.
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * 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