Yes, this is probably caused by a known bug in 4.6 that has been fixed for a month or two and mentioned in the release notes. Some work-arounds are suggested here http://redmine.gromacs.org/issues/1249, but you should probably update to 4.6.3 :-)
Mark On Wed, Jul 10, 2013 at 5:43 PM, Cristina Dezi <cristina.d...@gmail.com> wrote: > Dear users, > > I am performing MD simulations of short peptides (from 7 to 45 units) in > implicit solvent. I found quite bizarre results: all peptides unfold after > few picosends, adopting a rather linear conformation until the end of MD, > irrespective of temperature (I performed simulations at 200K, 400K and 600K > for 50 ns). I am wondering if these results do have any sense, as they are > very different from what I found with similar MD in gas phase, explicit > solvent (water) and also from what is published in literature to the date. > > I searched the forum archives and found the different issues related with > implicit solvent but maybe I missed something, I would be very grateful if > some of you with more experience with GROMACS (I have experience expecially > with AMBER and explicit solvents) could take some time to check my input > file to see if I made some mistake. I am using GROMACS version 4.6. > > Thank you very much in advance for your help, > > Kindest regards > > Cristina Dezi, PhD > > Chemistry Department, > CINVESTAV > Av. Instituto Politecnico Nacional, 2508 > A.P. 14-740 Mexico D.F. 07000 > MEXICO > > *INPUT FILE* > integrator = md > nsteps = 2500000 > dt = 0.002 > comm-mode = ANGULAR > nstxout = 5000 > nstvout = 5000 > nstenergy = 5000 > nstlog = 5000 > continuation = no > vdw-type = Cut-off > nstlist = 0 > ns_type = simple > pbc = no > rlist = 0.0 > rlistlong = 0.0 > coulombtype = cut-off > rcoulomb-switch = 0 > rcoulomb = 0.0 > rvdw = 0.0 > rvdw-switch = 0.0 > tcoupl = nose-hoover > tc-grps = system > tau_t = 0.4 > ref_t = 200 > pcoupl = no > gen_vel = yes > gen_temp = 200 > gen_seed = 290389 > implicit_solvent = GBSA > gb_algorithm = Still > nstgbradii = 1 > rgbradii = 0 > gb_epsilon_solvent = 80 > gb_saltconc = 0 > sa_algorithm = Ace-approximation > sa_surface_tension = 2.05016 > -- > 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
