[gmx-users] so difficult problem

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jan 6 20:50:39 CET 2011

Hi Mohsen,

I think rotating a molecule with editconf will not rotate the box. Then
again, if it did, it would result in a box violating Gromacs requirements.
Either way, it's not going to work like that. Build a new box after
rotation... And have a good look at what you're actually trying now by
taking the rotated system and stack it a few times using genconf -nbox 2 2 2



On Jan 6, 2011 7:22 PM, "mohsen ramezanpour" <ramezanpour.mohsen at gmail.com>

Dear Amit
I entered these commands for rotating box:
editconf   -f  conf.gro  -o  output.pdb   -rotate  0   0  25.4
and then:
editconf   -f output.pdb  -o  newbox.pdb   -rotate   0  127.67548  0
as a result my molecul is located out of box totally,of course drug and
protein are bind to eachother yet.
thanks in advance for your attention and reply

On Tue, Jan 4, 2011 at 1:25 PM, Amit Choubey <kgp.amit at gmail.com> wrote: > >
Could you post the e...

gmx-users mailing list    gmx-users at gromacs.org
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.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110106/01407607/attachment.html>

More information about the gromacs.org_gmx-users mailing list