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

[Pedro Lacerda]

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.

Can a .top file have a molecule where not all atoms are bonded?


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
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>>> University of Maryland, Baltimore
>>> 20 Penn St.
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>>>
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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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