[gmx-users] Vizualization of lipid protein system

[James Starlight]

I guess for my case this should work

3 If you want jumps removed, extract the first frame from the
trajectory to use as  reference, and then use trjconv -pbc nojump with
that first frame as reference

hovewer in my case the VMD movie looks like all solvent molecules are
spread from the protein in all directions.


2016-03-14 12:50 GMT+01:00 James Starlight <jmsstarlight at gmail.com>:
> 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