Dear gmx-users, I'm trying to do a mild minimization on a homohexameric protein in vacuo. I used the following options in the em.mdp file:
title = mild-mini cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = steep nsteps = 500 emtol = 5000 emstep = 0.1 nstcomm = 1 ns_type = grid nstlist = 5 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 = 4 ewald_rtol = 1e-5 optimize_fft = yes I simply converted my protein from .pdb format to .gro using pdb2gmx, and then I submitted immediately to minimization, since I only would like to relieve some eventual steric clashes between subunits, without proceed with a further MD simulation and without distorting too much the protein structure. At the end of the run I found that the 6 subunits of my protein (which are not covalently linked to each others) are separated in two dimers and two monomers. I tried also the minimization in water, although for this system I don't want water, but the result is not changing: the protein separates in subunits. The same if I apply PBC (the first time I applied it, then I saw that the subunits separated, I check the gmx-users list and delete pbc from the em.mdp, but the results are quite the same). I also changed ns_type to simple, without success. Have you got any suggestion? Thanks in advance Anna ______________________________________________ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: [email protected] Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm ____________________________________________________ "If you think you are too small to make a difference, try sleeping with a mosquito" _______________________________________________ gmx-users mailing list [email protected] http://www.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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
