Sorry, but I couldnt get your question, I have used this .mdp file for energy minimisation after addition of water and using GROMOS96 43a1 force field : title = drg_trp cpp = /lib/cpp ; location of cpp on SGI define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4] constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 2000 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME ; Use particle-mesh ewald rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01
I hope it will help you to guide me further Thanks -- Sonali Dhindwal --- On Wed, 19/5/10, Erik Marklund <er...@xray.bmc.uu.se> wrote: From: Erik Marklund <er...@xray.bmc.uu.se> Subject: Re: [gmx-users] enegry minimisation To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Date: Wednesday, 19 May, 2010, 5:31 PM sonali dhindwal skrev: > 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. > 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. > 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. > Thanks and regards > ^ > > > -- > Sonali Dhindwal > > So how has your system setup changed since your previous EM? Addition of water? Cutoffs? PME? -- ----------------------------------------------- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 er...@xray.bmc.uu.se http://folding.bmc.uu.se/ -- 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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