[gmx-users] Fwd: Re: Dimeric structure strangely separated

Thu Jun 16 02:48:20 CEST 2016

I just did trjconv with `-pbc nojump` and now the RMSD looks right. I would
never expected that. It works!

My 2+ ion is using parameters for nonbonded model without charge transfer
found in this paper:
J Chem Theory Comput. 2013 June 11; 9(6): 2733–2748. doi:10.1021/ct400146w.

This may be useful for people doing runs with metallic nonbonded 2+ ions.
*https://docs.google.com/spreadsheets/d/1pzBJU5QP5j4XRtEbN4htQ8j8_GU73G3ZYvkG1YZDKWc/edit?usp=sharing
<https://docs.google.com/spreadsheets/d/1pzBJU5QP5j4XRtEbN4htQ8j8_GU73G3ZYvkG1YZDKWc/edit?usp=sharing>*

Some approaches do a charge correction redistributing it at the ion
ligands, but I can't afford it.
    Journal of Structural Biology 157 (2007) 444–453

I'm worried because my ion has coordination number 4 or 5, probably
requiring charge transfer what is beyond my abilities. So i'm accepting
suggestions on how to manage my ion.

2016-06-15 12:29 GMT-03:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 6/15/16 10:25 AM, Pedro Lacerda wrote:
>
>> Very thank you, Justin.
>>
>> So is just the system that is very unstable.
>>
>>
> Not necessarily.  Have you tried fitting with trjconv?  I haven't gotten a
> clear answer on that.  Forget VMD centering, gmx rms -nopbc, etc.  Have you
> used trjconv and gotten a "clean" trajectory with no jumps or broken
> molecules?  If not, try it.
>
> Noob questions follows.
>>
>> But here other similar system where shows what I expect when the molecule
>> is across the boundary. This isn't happening in the previous plot.
>>
>>     gmx rms -s md.tpr -f md.xtc -pbc
>>     http://postimg.org/image/69fafxdx7/
>>
>>     gmx rms -s md.tpr -f md.xtc -nopbc
>>     http://postimg.org/image/swujm2th7/
>>
>> Another small question, my metallic ion is attached to the protein even if
>> i'm using the nonbonded model. So the interaction site is already
>> favorable
>> even if not bonded. Now I'm doing the bonded model parametrization but
>> from
>> your experience this has huge impact? Distances and angles will be
>> preserved, or I really need to try both models and compare?
>>
>>
> Metal ions are notoriously hard to deal with in an additive
> representation, especially if they are 2+ or larger.  Check the literature
> for similar systems.
>
> -Justin
>
>
>
>>
>>
>> 2016-06-15 10:54 GMT-03:00 Justin Lemkul <jalemkul at vt.edu>:
>>
>>
>>>
>>> On 6/15/16 9:49 AM, Pedro Lacerda wrote:
>>>
>>> PBC is always considered by default at Gromacs analysis tools, and I
>>>> recentered following the standard VMD procedure.
>>>> Considering the PBC, the animation looks quite right to me.
>>>>
>>>>
>>>> Well, sure - PBC doesn't care about visualization convenience, but the
>>> molecule is clearly "broken" across a boundary at t=0 and you get a huge
>>> RMSD at this point with respect to whatever your starting conformation
>>> (presumably unbroken, and likely centered) is.  Thus, the value is
>>> "correct" but probably not truly reflective of what the actual values
>>> should be.
>>>
>>> Can a .top file have a molecule where not all atoms are bonded?
>>>
>>>>
>>>>
>>>> Of course.
>>>
>>> -Justin
>>>
>>>
>>>
>>> 2016-06-15 10:39 GMT-03:00 Justin Lemkul <jalemkul at vt.edu>:
>>>>
>>>>
>>>>
>>>>> On 6/15/16 9:35 AM, Pedro Lacerda wrote:
>>>>>
>>>>> Thank you,
>>>>>
>>>>>>
>>>>>> I never did it before but I'll try it. And at VMD I recentered the
>>>>>> molecule. And looks right to you so much deviation even at the
>>>>>> begining?
>>>>>> Never happened to me!
>>>>>>
>>>>>>
>>>>>> You're calculating the RMSD of a broken molecule; the animation shows
>>>>>>
>>>>> that
>>>>> quite clearly.  You shouldn't do that.
>>>>>
>>>>> One more question. What happens when two molecules are put as one
>>>>> molecule
>>>>>
>>>>> in .top, like a molecule that are two disjoints graphs or two
>>>>>> molecules.
>>>>>> Seems to work fine.
>>>>>>
>>>>>>
>>>>>> I don't understand what you're asking here.
>>>>>>
>>>>>
>>>>> -Justin
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> 2016-06-15 10:00 GMT-03:00 Justin Lemkul <jalemkul at vt.edu>:
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 6/15/16 8:45 AM, Pedro Lacerda wrote:
>>>>>>>
>>>>>>> Hi list,
>>>>>>>
>>>>>>>
>>>>>>>> RMSD analysis of trajectories differs very much from the intuition
>>>>>>>> gained
>>>>>>>> with the visual inspection of trajectories. RMSD has almost 4nm
>>>>>>>> while
>>>>>>>> the
>>>>>>>> video seems correct.
>>>>>>>>
>>>>>>>> I'm using Amber 14ffSB with an metallic nonbonded ion attached on
>>>>>>>> it.
>>>>>>>> It
>>>>>>>> was converted from Amber files using ACPYPE, the initial structure
>>>>>>>> seems
>>>>>>>> correct and the problem doesn't seems originated in parametrization
>>>>>>>> errors.
>>>>>>>>
>>>>>>>> Please can you point me some directions to debug this defect? I
>>>>>>>> guess
>>>>>>>> that
>>>>>>>> isn't needed but do I need to attach some relevant file?
>>>>>>>>
>>>>>>>> Look at the picture of the animation and RMSD of the first 2ns
>>>>>>>> trajectory:
>>>>>>>>
>>>>>>>>     http://imgur.com/a/bFCr8
>>>>>>>>
>>>>>>>> Please wait for full loading the animated gif, the remaining of the
>>>>>>>> .xtc
>>>>>>>> look like this first 20s of the gif. The RMSD was taken with the
>>>>>>>> -nopbc
>>>>>>>> option! If taken without -[no]pbc flag the plot breaks like if PBC
>>>>>>>> was
>>>>>>>> not
>>>>>>>> considered. It looks like quite the opposite from the expected,
>>>>>>>> right?
>>>>>>>>
>>>>>>>> I also measured the RMSD using VMD giving the same results. Maybe
>>>>>>>> this
>>>>>>>> is
>>>>>>>> a
>>>>>>>> very simple error, what can I doing wrong?
>>>>>>>>
>>>>>>>>
>>>>>>>> Use trjconv to recenter and make your molecules whole.  That's
>>>>>>>> standard
>>>>>>>>
>>>>>>>> practice before computing RMSD.  I have had mixed results with
>>>>>>> -nopbc
>>>>>>> and
>>>>>>> do not rely on it.
>>>>>>>
>>>>>>> -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
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>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>> ==================================================
>>>>>
>>>>> 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
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>>>>>
>>>>> --
>>> ==================================================
>>>
>>> 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
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> --
> ==================================================
>
> 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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> Gromacs Users mailing list
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