[gmx-users] First frame already out of box, getting very large RMSD

[yunshi11 .]

On Sat, Feb 28, 2015 at 4:40 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/28/15 7:38 PM, yunshi11 . wrote:
>
>> On Sat, Feb 28, 2015 at 4:21 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 2/28/15 7:17 PM, yunshi11 . wrote:
>>>
>>>  On Sat, Feb 28, 2015 at 3:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>
>>>>> On 2/28/15 6:00 PM, yunshi11 . wrote:
>>>>>
>>>>>   Dear all,
>>>>>
>>>>>>
>>>>>> I am running MD for a protein-ligand complex in a dodecahedron box and
>>>>>> followed the "Suggested trjconv workflow" from
>>>>>> http://www.gromacs.org/Documentation/Terminology/
>>>>>> Periodic_Boundary_Conditions
>>>>>> .
>>>>>>
>>>>>> Now I wonder how to remove jumps (across periodic boxes) when the
>>>>>> first
>>>>>> frame (actually the .gro file from equilibration run) is already
>>>>>> jumping
>>>>>> across two (or more) boxes (according to visualization in VMD).
>>>>>>
>>>>>> I understand that this is just an visualizing artifact, but it seems
>>>>>> to
>>>>>> also affect other analyses such as calculations of RMSD along the
>>>>>> trajectory. I got some impossible RMSD values like 1.5 nm, considering
>>>>>> other replicate simulations give only ~0.3 nm.
>>>>>>
>>>>>> Any idea on how to fix this (the effect on RMSD calculations etc., not
>>>>>> visualization)?
>>>>>>
>>>>>>
>>>>>>   trjconv -center -pbc mol -ur compact usually solves all problems for
>>>>>>
>>>>> such
>>>>> simple systems.  Center on the protein, everything else gets re-wrapped
>>>>> around it. More complex operations would be needed for protein
>>>>> complexes,
>>>>> membranes, etc. But proteins in water (with or without ligands) are
>>>>> generally straightforward.
>>>>>
>>>>>
>>>>>   I did try that, and other combinations of -pbc and -ur options. Sorry
>>>>>
>>>> that
>>>> I should have been more specific:
>>>>
>>>> My system is a homo dimer of protein, each with two ligands (cofactor +
>>>> inhibitor) bound symmetrically. Some trjconv options can put the dimer
>>>> protein together, but the two ligands of the second monomer are always
>>>> in
>>>> the other periodic boxes.
>>>>
>>>>
>>>>  This changes the approach considerably; always provide full details in
>>> the
>>> first message - you'll arrive at a solution faster!
>>>
>>> The centering in this case should be done with respect to one protein or
>>> some chosen custom group of residues that makes a logical center (e.g.
>>> the
>>> interfacial residues of one subunit).  The same concept applies - the
>>> remaining elements of the system (the other protein, the ligands, etc)
>>> will
>>> be wrapped with respect to the centered subunit.
>>>
>>>
>>>  With trjconv -s x.tpr -f x.gro -n x.ndx -center -pbc mol -ur compact -o
>> x.gro, I tried centering on monomer A, monomer B, and two interfacial
>> residues of monomer A. None of them worked, and the two ligands of monomer
>> B are always outside the box.
>>
>> Can I send .gro files to the mailing list?
>>
>>
> No. To share files you need to upload them to a file-sharing service and
> provide a link.  The input files (.tpr, .gro, and .ndx) would be useful.
>
>
> Please have a look at these files at
https://drive.google.com/folderview?id=0B8xuDbuW-ACESnlTcUVrUEdKSGs&usp=sharing

Please make the .tpr file with the .mdp, .top, and .gro files provided,
since different versions of gromacs may not be compatible with all .tpr
file versions.

Thanks,
Yun


> -Justin
>
> --
> ==================================================
>
> 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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