[gmx-users] Vizualization of lipid protein system

James Starlight jmsstarlight at gmail.com
Mon Mar 14 12:50:55 CET 2016

forgot to add

if I use

-fit rot+trans

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


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

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