[gmx-users] Vizualization of lipid protein system

[Justin Lemkul]

On 3/14/16 7:55 AM, James Starlight wrote:
> 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.
>

...which is precisely what -pbc nojump does.  If you want things back in the 
box, you need e.g. -pbc mol.  You have a complex system, it requires a complex 
(multi-step) solution to render it appropriately.

-Justin

>
> 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

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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