bharat gupta wrote:
Thanks for ur kind reply Justin ...
I also searched the gmx userlist regarding the same query and I found
out that It was mentioned to repeat the simulation again with a
different force field .. but I don't know about the energy minimization
parameters as I am following ur lysozyme tutorial for that .. I will
get back to u get if I get the same type of structural changes with this
force field...
Also I would like to mention one more thing .. as I did the simulation
of crystal str of GFP with the same parameters which I used for the
variant of GFP .. In case of the crystal str. simulation result, it
seems to be perfectly fine and there is no change in the secondary
structure also ... So, if I am not wrong then there is some problem with
the variant structure that I have modeled ??.. Actually the variant of
GFP that I have modeled has one loop (of 4 amino acid in original str)
replaced with an another loop of 9 residues length ... CAn this be the
reason ??
You cannot draw any sort of reliable conclusions from a single trajectory of
such short length.
Regarding the simulation time I want to ask ... what is the minimum or
the optimal time the structure should be simulated for such analysis as
I have read many paper published in big journals doing simulation only
for 1ns (in that case I am doing for 3 ns)... pls comment
There is no hard and fast rule for how long an MD simulation needs to be. You
need to collect sufficient data over a sufficient time period to model the
behavior of interest, with the understanding of how long it should take for that
certain phenomenon to occur. Expectations also scale with the quality of the
software and hardware. The paper you linked before was from 1999, at which time
the expectations of simulation length were exponentially shorter. Most systems
aren't even completely stable after only 1 ns of unrestrained MD. Nowadays, 1
ns can be completed in a matter of hours, so the expectation (by reviewers and
journals) is that far more data can be collected such that you approach a
biologically-relevant time scale.
For loop movement, 3 ns is at least 10 times too short, in my experience. 50 or
100 ns would be more appropriate, but don't just take my word for it. You
should also conduct independent simulations (i.e., different starting velocities
applied to the same structure) to run multiple simulations and do proper
statistical analysis. You wouldn't do one single assay at the bench, so why
would you do one single simulation and expect it to be absolutely correct? It
is possible that a single simulation shows erroneous behavior and can be
eliminated as an outlier with sufficient replicates and data analysis.
-Justin
On Wed, Feb 2, 2011 at 3:34 AM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
bharat gupta wrote:
Hi,
I think I have asked this question earlier in the forum .. that
during my 3ns simulation of a 230 amino acid proteins some
portion of 2 beta strands got converted to loop/random coil,
after visualizing in VMD. I checked the DSSP profile also .. and
as per the DSSP results it's coil in that region .. can anybody
tell me where can the error be as I have been checking my
structure right from the minimization step till npt
equilibration and its was fine ... this has happened only after
simulation ... pls help ??
The comments I made last week still stand:
http://lists.gromacs.org/pipermail/gmx-users/2011-January/058014.html
You're basing your conclusions on a 3-ns simulation, which I would
say is far too short to obtain any meaningful data for such a system.
-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 : [email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
--
========================================
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 : [email protected] <mailto:[email protected]>
--
========================================
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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