[gmx-users] so difficult problem

[Tsjerk Wassenaar]

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

Cheers,

Tsjerk

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

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...

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