[gmx-users] Vizualization of lipid protein system

[James Starlight]

Right, thank you!
probably I need to combination of -pbc mol and -pbc nojump in the
sequence order.

2016-03-14 12:57 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
> 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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