Thanks Justin for your reply. Yes I have included solvent in the protein using genbox. I am pasting .mdp file which I used for MD simulation :
title = trp_drg MD cpp = /lib/cpp ; location of cpp on SGI constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 500000 ; total 1 ns. nstcomm =1 nstxout = 500 ; output coordinates every 1.0 ps nstvout =0 nstfout =0 nstlist = 5 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.4 fourierspacing = 0.12 fourier_nx =0 fourier_ny =0 fourier_nz =0 pme_order =6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 0.1 0.1 0.1 tc_grps = Protein SOL MG PEP E4P NA+ ref_t = 300 300 300 300 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 I hope it will help you to guide me futher. Thanks -- Sonali Dhindwal --- On Wed, 19/5/10, Justin A. Lemkul <jalem...@vt.edu> wrote: From: Justin A. Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] enegry minimisation To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Date: Wednesday, 19 May, 2010, 5:17 PM sonali dhindwal wrote: > Hello All > This question may sound trivial to many, but as i am new to this field, > please help. > I want to ask a question regarding my previous query of distortion of protein > strucutre after molecular dynamcs simulation. Can you provide a link to your previous post, for reference? > I have noticed that after enegry minimisation using steepest decent > algorithm, using emtol of 1000 kJ mol^-1 nm^-1 . > 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. 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. 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. -Justin > Thanks and regards > ^ > > -- > Sonali Dhindwal > > -- ======================================== 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@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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