[gmx-users] Vizualization of lipid protein system

James Starlight jmsstarlight at gmail.com
Mon Mar 14 12:48:05 CET 2016

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



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