<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Sorry, but I couldnt get your question,<br>I have used this .mdp file for energy minimisation after addition of water and using <pre style="margin: 0em;">GROMOS96 43a1 force field :</pre><br>title = drg_trp<br>cpp = /lib/cpp ; location of cpp on SGI<br>define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4]<br>constraints = none<br>integrator = steep<br>dt = 0.002 ; ps !<br>nsteps =
2000<br>nstlist = 10<br>ns_type = grid<br>rlist = 0.9<br>coulombtype = PME ; Use particle-mesh ewald<br>rcoulomb = 0.9<br>rvdw = 1.0<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>;<br>; Energy minimizing stuff<br>;<br>emtol =
1000.0<br>emstep = 0.01<br><br>I hope it will help you to guide me further<br>Thanks<br><div>--<br>Sonali Dhindwal</div><br><br>--- On <b>Wed, 19/5/10, Erik Marklund <i><erikm@xray.bmc.uu.se></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Erik Marklund <erikm@xray.bmc.uu.se><br>Subject: Re: [gmx-users] enegry minimisation<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Wednesday, 19 May, 2010, 5:31 PM<br><br><div class="plainMail">sonali dhindwal skrev:<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>> I have noticed that after enegry minimisation using
steepest decent algorithm, using emtol of 1000 kJ mol^-1 nm^-1 , large amount of distortion occurs.<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>> Thanks and regards<br>> ^<br>> <br>> <br>> --<br>> Sonali Dhindwal<br>> <br>> <br>So how has your system setup changed since your previous EM? Addition of water? Cutoffs? PME?<br><br>-- -----------------------------------------------<br>Erik Marklund, PhD student<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: +46 18 471 4537 fax: +46 18 511 755<br><a ymailto="mailto:erikm@xray.bmc.uu.se" href="/mc/compose?to=erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a
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