bharat gupta wrote:
Since the paper that I am following says that for that protein (GFP) 1ns
simulation is enough as other people carried out 10ns for the same
protein and rmsd follows the same pattern which is being shown by that
1ns simulation ..
When were those studies published? With modern hardware and a recent Gromacs
version, you can get 10 ns is two days' time, and the data you collect
represents a time scale well below most biologically-relevant events except the
smallest of motions. A paper that did only 1 ns should be fairly old, I imagine.
So I decided to do a 3ns simulation .... the RMSD that I got was same as
that mentioned in the paper ... showing that the barrel doesnot show
much fluctuation and remains stable for a 3ns simulation (similar to
that 1ns one).
Again I decided to go for 10 ns simulation this time but I changed the
force field this time ... I got a different trajectory ...
All trajectories (theoretically, if starting from independent velocities) are
"different." You can't expect everything to be identical, especially over short
time periods. Multiple replicates over long time frames should converge to some
meaningful averages of the observables of interest. Time averages would equal
ensemble averages once the initial "memory" of the system is lost. This is
ergodicity.
What shall I do now ?? .. shall I repeat that 10ns simulation with the
same FF that I was using for 3ns simulation ??
You should do your homework about which force field model you believe should be
most accurate, basing your choice on (1) papers that have studied the same or
similar systems and (2) systematic comparisons of force fields to understand
their inherent limitations and benefits. There are several such papers that
have come out in recent years, some more complete than others. The results of
(2) should supersede the results of (1): if a group used force field X on system
Y, but then force field X was later shown to incorrectly reproduce some
important aspect of system Y, then force field X is probably a bad choice, even
if there is some element of precedent.
-Justin
On Tue, Feb 22, 2011 at 6:31 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
bharat gupta wrote:
Hi
I did a simulation of 3 ns with OPLS AA 2001 Force Field for a
protein of 230 aa and also I carried out a simulation of 10ns
for the same protein but with different force field (Amber 2006)
. I obtained the rmsd of the trajectories of both simulation ,
which I found to be different ?? i.e. 3ns rmsd from one
simulation doesnot superimpose with another (10ns) .. why there
is such a difference ??
Different force fields can give different results, unfortunately.
There are several comparisons in the literature among common force
fields. Understanding inherent limitations and assumptions in each
model is an important (read: absolutely critical) part of designing
a simulation.
Also realize that you're comparing an extremely short (3 ns)
trajectory with a moderately short (10 ns) one. In theory,
exhaustive sampling (i.e. orders of magnitude larger than what
you've done) should converge over all simulations. But due to the
inherent differences in parameter sets, this is unlikely to be the
case. The fact that your simulations are so short probably
magnifies this effect.
-Justin
--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com>
<mailto:monu46...@yahoo.com <mailto:monu46...@yahoo.com>>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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