<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><div id="yiv95151640">Thanks Justin for your help<br>I checked the mdout.mpd, all the parameters were interpereted correctly, though from next time i will take care of putting space.<br>regarding you asked if those are small molecules, yes those are the ligands and i have taken .itp and .gro file from Dundee Prodrg server. I think those are acceptable !!<br>Thermostat setup:<br>I will now do this thing seperately as protein and non protein only as given in manual.<br><br>And also I will do that thing suggested by Gaurav, hopefully it will help in not distorting the protein structure.<br>Thanks a lot.<br><br><div>--<br>Sonali Dhindwal</div><br><br>--- On <b>Wed, 19/5/10, Justin A. Lemkul <i><jalemkul@vt.edu></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Justin A. Lemkul
<jalemkul@vt.edu><br>Subject: Re: [gmx-users] enegry minimisation<br>To: "Gromacs Users' List" <gmx-users@gromacs.org><br>Date: Wednesday, 19 May, 2010, 5:45 PM<br><br><div class="plainMail"><br><br>sonali dhindwal wrote:<br>> Thanks Justin for your reply.<br>> Yes I have included solvent in the protein using genbox.<br><br>Then you should do energy minimization after constructing the system.<br><br>> I am pasting .mdp file which I used for MD simulation :<br>> <br>> title = trp_drg MD<br>> cpp = /lib/cpp ; location of cpp on SGI<br>> constraints = all-bonds<br>> integrator = md<br>> dt = 0.002 ; ps !<br>> nsteps
= 500000 ; total 1 ns.<br>> nstcomm =1<br><br>I don't know if this matters or not, but I think your parameters and values
should be separated from the '=' by whitespace. I also don't know if that will have any effect on your unstable system (see below), but do check to make sure that all of your settings have been interpreted correctly. Confirm your input settings with the mdout.mdp file produced by grompp.<br><br>> nstxout = 500 ; output coordinates every 1.0 ps<br>> nstvout =0<br>> nstfout =0<br>> nstlist = 5<br>> ns_type = grid<br>> rlist = 0.9<br>> coulombtype = PME<br>> rcoulomb = 0.9<br>> rvdw
= 1.4<br>> fourierspacing = 0.12<br>> fourier_nx =0<br>> fourier_ny =0<br>> fourier_nz =0<br>> pme_order =6<br>> ewald_rtol = 1e-5<br>> optimize_fft = yes<br>> ; Berendsen temperature coupling is on in four groups<br>> Tcoupl = berendsen<br>> tau_t = 0.1 0.1 0.1 0.1 0.1 0.1<br>> tc_grps = Protein SOL MG PEP E4P NA+<br>> ref_t =
300 300 300 300 300 300<br><br>This thermostat setup is certainly incorrect. You should not couple all the components of your system to separate thermostats. See here:<br><br><a rel="nofollow" target="_blank" href="http://www.gromacs.org/Documentation/Terminology/Thermostats">http://www.gromacs.org/Documentation/Terminology/Thermostats</a><br><br>You have a fairly complicated system. Are some of these species small molecules? If so, how did you derive their parameters? Have you demonstrated that these parameters are accurate? Which structure is falling apart, and how are you making that assessment?<br><br>-Justin<br><br>> ; Pressure coupling is on<br>> Pcoupl = berendsen<br>> pcoupltype = isotropic<br>> tau_p
= 0.5<br>> compressibility = 4.5e-5<br>> ref_p = 1.0<br>> ; Generate velocites is on at 300 K.<br>> gen_vel = yes<br>> gen_temp = 300.0<br>> gen_seed = 173529<br>> <br>> I hope it will help you to guide me futher.<br>> Thanks<br>> <br>> --<br>> Sonali Dhindwal<br>> <br>> <br>> --- On *Wed, 19/5/10, Justin A. Lemkul /<<a rel="nofollow">jalemkul@vt.edu</a>>/* wrote:<br>> <br>> <br>> From: Justin A. Lemkul <<a rel="nofollow">jalemkul@vt.edu</a>><br>> Subject: Re: [gmx-users] enegry minimisation<br>> To: "Discussion list for GROMACS users" <<a rel="nofollow">gmx-users@gromacs.org</a>><br>> Date: Wednesday, 19 May, 2010, 5:17
PM<br>> <br>> <br>> <br>> sonali dhindwal wrote:<br>> > Hello All<br>> > This question may sound trivial to many, but as i am new to this<br>> field, please help.<br>> > I want to ask a question regarding my previous query of<br>> distortion of protein strucutre after molecular dynamcs simulation.<br>> <br>> Can you provide a link to your previous post, for reference?<br>> <br>> > I have noticed that after enegry minimisation using steepest<br>> decent algorithm, using emtol of 1000 kJ mol^-1 nm^-1 .<br>>
> So is it necessary to do enegry minimisation step before MD,<br>> because this is my modeled protein, and i have already done energy<br>> minimisation using different program and after that I have done<br>> refinement also.<br>> <br>> Have you added solvent or anything else to the protein model? If<br>> so, then the answer is yes. Solvation with a regularly-ordered<br>> lattice of solvent molecules can (and often does) lead to bad<br>> clashes with your protein structure, thus necessitating further<br>> minimization.<br>> <br>> There are plenty of reasons why a protein structure might be<br>> unstable, most of them related to .mdp file settings, but
you<br>> haven't posted those so there's no way to know if you're doing<br>> things correctly.<br>> <br>> -Justin<br>> <br>> > Thanks and regards<br>> > ^<br>> ><br>> > --<br>> > Sonali Dhindwal<br>> ><br>> ><br>> <br>> -- ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>>
jalemkul[at]vt.edu | (540) 231-9080<br>> <a rel="nofollow" target="_blank" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>> <br>> ========================================<br>> -- gmx-users mailing list <a rel="nofollow">gmx-users@gromacs.org</a><br>> </mc/compose?to=<a rel="nofollow">gmx-users@gromacs.org</a>><br>> <a rel="nofollow" target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a rel="nofollow" target="_blank" href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before<br>> posting!<br>>
Please don't post (un)subscribe requests to the list. Use the www<br>> interface or send it to <a rel="nofollow">gmx-users-request@gromacs.org</a><br>> </mc/compose?to=<a rel="nofollow">gmx-users-request@gromacs.org</a>>.<br>> Can't post? Read <a rel="nofollow" target="_blank" href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>> <br>> <br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia
Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a rel="nofollow" target="_blank" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- gmx-users mailing list <a rel="nofollow">gmx-users@gromacs.org</a><br><a rel="nofollow" target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a rel="nofollow" target="_blank" href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a rel="nofollow">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a rel="nofollow" target="_blank"
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