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