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 <jalem...@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 <jalem...@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 <jalem...@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
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Justin A. Lemkul, Ph.D.
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Department of Pharmaceutical Sciences
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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
jalem...@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
jalem...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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