[gmx-users] Vizualization of lipid protein system

[James Starlight]

forgot to add

if I use

-fit rot+trans

the system looks fine BUT moves as a whole like a propeller =))

J.

2016-03-14 12:48 GMT+01:00 James Starlight <jmsstarlight at gmail.com>:
> Dear all!
>
> I am looking for the possibility to vizualize my long md trajectory
> for the receptor embedded in the membrane
>
> If I just load the trajectory to vmd there is no problem with the
> exeption that receptor moves laterally along the membrane resulting at
> the end in PBC artifacts
>
> If It try to post-process the trajectory by the following method
>
> g_trjconv -s minimization.gro -f production_run_gpcr_CG -dt 10 -b 100
> -o traj.dcd  -pbc nojump
>
> the system now becomes centred on the receptor but all lipids now are
> fly away from the receptor which looks not very good for me =)
>
>
> how I could prevent those artifacts making vizualisation properly7
>
> Thanks!
>
> James