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

[yunshi11 .]

On Sun, Mar 1, 2015 at 11:43 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/1/15 1:21 PM, yunshi11 . wrote:
>
>> 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.
>>
>>
> Well, I have just about every GROMACS version available to me, and you
> could just tell me what version you're using.  There's a reason I want to
> see your .tpr file; its contents are part of the consistency check I want
> to do. Moreover, all I'm going to get by using these files is generate a
> .tpr with the coordinates from nvt.gro; there's no purpose to fitting this
> structure to itself and there's no way to check anything this way.
>
> Please provide the .tpr, as requested, as well as provide the *exact*
> command you're using (no "x" substitutions; I need to know exactly what
> you're doing if you want me to try to reproduce or fix it).
>
>
I tried many commands that did not work, and the most recent one is:

trjconv -s nvt.tpr -f nvt.gro -pbc mol -center -ur compact -n chain.ndx -o
nvt2.gro, with selected indexes as:

Select group for centering
......
Select a group: 36
Selected 36: 'enzymeA'
Select group for output
......
Select a group: 32
Selected 32: 'dimtprz'


Note nvt.tpr is generated with em2.gro, a structural file with no
periodicity and looks alright, and nvt.gro is the output from running
nvt.tpr

Please refer to the same link (updated files): https://drive.google.com/
folderview?id=0B8xuDbuW-ACESnlTcUVrUEdKSGs&usp=sharing


>
> -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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