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

[Justin Lemkul]

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

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