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

[Justin Lemkul]

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
>>>>>>
>>>>>> ==================================================
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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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>>>>
>> --
>> ==================================================
>>
>> 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
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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

==================================================