[gmx-users] Re: change in secondary structure
bharat gupta
bharat.85.monu at gmail.com
Wed Feb 2 14:24:09 CET 2011
Thanks for such a detailed reply to my queries .. But conducting a 50ns
simulation will take time ... so i want to conduct independent simulation
and for that I searched some threads but was not able to get the proper
description and method... if u can guide me through an appropriate link ..
it would be much more helpful ..
On Wed, Feb 2, 2011 at 5:10 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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 <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> 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 : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
>> <mailto:monu46010 at yahoo.com <mailto:monu46010 at 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 : monu46010 at yahoo.com <mailto:monu46010 at 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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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 : monu46010 at yahoo.com
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