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 <[email protected]> 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 <[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 >> >> ======================================== >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [email protected] >> <mailto:[email protected]>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- >> 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 > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- 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]
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