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

Mon Mar 2 02:26:31 CET 2015

On Sun, Mar 1, 2015 at 4:36 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/1/15 3:47 PM, yunshi11 . wrote:
>
>> 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
>>
>>
> trjconv -s nvt.tpr -f nvt.gro -o nvt2.gro -pbc nojump
> trjconv -s nvt.tpr -f nvt2.gro -o nvt3.gro -n r_90_187.ndx -pbc mol -ur
> compact -center
>
> That works for me, though the index file you provided doesn't have
> anything called "enzymeA" so I used r_90_187 as the group for centering.
>
>
Alright:\  Is there a reason that you did not use -pbc whole before using
-pbc nojump?

But when I used your exact commands (assuming you selected the entire
system including solvents for -pbc nojump) for npt, it did not work (files
at the same link
https://drive.google.com/folderview?id=0B8xuDbuW-ACESnlTcUVrUEdKSGs&usp=sharing
).

trjconv -s npt.tpr -f npt.gro -o npt2.gro -pbc nojump
trjconv -s npt.tpr -f npt2.gro -o npt3.gro -n r_90_187.ndx -pbc mol -ur
compact -center

Does this mean I have to use nvt.tpr for fitting subsequent structural
files (.gro and .trr)?

> -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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>