Hi Mark I saw both the .gro file of hexane before and after EM in VMD as well checked their coordinates. I am not able to make anything out of it. it will better if one knows how to find the steric clash between two molecules?.
Regards Vinoth On Wed, Oct 6, 2010 at 11:08 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > > > ----- Original Message ----- > From: vinothkumar mohanakrishnan <kmvin...@gmail.com> > Date: Wednesday, October 6, 2010 15:20 > Subject: [gmx-users] Reg: Energy minimisation of hexane > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > > Hi all > > > > I am trying to simulate 150 molecules of hexane in a triclinic box > (8.319*3.01*3.01 nm^3) using OPLSAA force field.I got the .gro file from > PRODRG and generated the topology using X2top command. when i run energy > minimisation for hexane my potential energy is positve. is this right?. what > i should correct to get the potential energy as negative. below is my > result. any help is highly appreciated. > > > > Steepest Descents converged to Fmax < 100 in 10454 steps > > Potential Energy = 3.4133051e+04 > > Maximum force = 9.8812309e+01 on atom 635 > > Norm of force = 7.9230022e+00 > > So something is unhappy, and the minimizer can't deal with it. Probably you > have some massive steric clash, like two molecules overlying each other. > Look at the contents of your simulation cell before and after EM. > > Mark > > > > Below is my contents of my em.mdp file > > > > integrator = cg > > emtol = 100.0 > > emstep = 0.01 > > nsteps = 50000 > > nstcgsteep = 1000 > > nstlist = 1 > > ns_type = grid > > rlist = 1.0 > > coulombtype = PME > > fourierspacing = 0.12 > > rcoulomb = 1.0 > > rvdw = 1.0 > > pbc = xyz > > > > Regards > > Vinoth > > > > -- > > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists >
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