Hi there, I need a very simple em.mdp and md.mdp, to simply test my generated GMX files from ACPYPE.
It contains just a single small molecule without solvent. I just need to test if the topology file is OK (i.e. if grompp and mdrun will accept it), so I used to use these parameters with GMX 4: em.mdp: cpp = /usr/bin/cpp define = -DFLEXIBLE integrator = steep nsteps = 500 constraints = none emtol = 1000.0 emstep = 0.01 nstcomm = 1 ns_type = simple nstlist = 0 rlist = 0 rcoulomb = 0 rvdw = 0 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 1 pbc = no md.mdp: cpp = /usr/bin/cpp define = ;-DFLEXIBLE integrator = md nsteps = 500 constraints = none emtol = 1000.0 emstep = 0.01 comm_mode = angular ns_type = simple nstlist = 0 rlist = 0 rcoulomb = 0 rvdw = 0 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 1 pbc = no But these parameters won’t work anymore with GMX 5. Can someone suggest me the minimum alterations or completely new values so I could run a quick EM and MD? And if they were compatible to both GMX 4 and 5 that’d be great. Many thanks in advance, Alan -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.