<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Thanks Justin for your reply.<br>Yes I have included solvent in the protein using genbox.<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>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>; 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><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: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Wednesday, 19 May, 2010, 5:17 PM<br><br><div class="plainMail"><br><br>sonali dhindwal wrote:<br>> Hello All<br>> This question may sound trivial to many, but as i am new to this field, please help.<br>> I want to ask a question regarding my previous query of 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 decent algorithm, using emtol of 1000 kJ mol^-1 nm^-1 .<br>> So is it necessary to do enegry minimisation step before MD, because this is my modeled protein, and i have already done energy minimisation using
different program and after that I have done refinement also.<br><br>Have you added solvent or anything else to the protein model? If so, then the answer is yes. Solvation with a regularly-ordered lattice of solvent molecules can (and often does) lead to bad clashes with your protein structure, thus necessitating further minimization.<br><br>There are plenty of reasons why a protein structure might be unstable, most of them related to .mdp file settings, but you haven't posted those so there's no way to know if you're doing 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
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