[gmx-users] PBC problem in bilayer system

[Michael Carter]

Also if you want to fix the position on the centre of mass (no rotating or
translating) try

-pbc nojump

Followed by -fit rot+trans

Remember to use you new .xtc from your no jump command for the -fit
command. Then view in vmd and your molecules will not jump, rotate, or
translate around the box.

Mike

On 09/09/2014 15:12, "Michael Carter" <Michael.Carter at icr.ac.uk> wrote:

>Hi,
>
>Try -pbc nojump
>
>Best,
>Mike
>
>On 09/09/2014 15:11, "shahab shariati" <shahab.shariati at gmail.com> wrote:
>
>>Dear gromacs users
>>
>>I did MD simulation of my system containing DPPC lipids + water molecule
>>and 4 drug molecules.
>>
>>I saw trajectory file using VMD.
>>
>>Unfortunately, drug molecules jump across the box.
>>
>>How to resolve this PBC problem?
>>
>>which of -pbc options (none, mol, res, atom, nojump, cluster or whole) in
>>trjconv tool is appropriate for my case?
>>
>>
>>Any help will highly appreciated.
>>-- 
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