The problem could be gen_vel=no if you are not loading velocities that are consistent with your production temperature of 200 K. If, for example, you do not load any velocities at all, then the initial forces will quickly be scaled up to reach 200 K and this can cause large scale deformations/rearrangements.
There are a number of other strange things (like nstlist=5 with dt=0.0005 -- nstlist seems unnecessarily frequent, the 200 K temperature, and your use of separate temperature coupling groups which does not give the correct ensemble). Still, those are tangents to your main question. Nevertheless, if you don't have time to run any more simulations (as you stated earlier) then none of this is really going to help you. If, on the other hand, you do have time to run other simulations, then I still think you should start with repeating your result. Chris. -- original message -- I guess you want to see the production mdp file. Here it is: ; VARIOUS PREPROCESSING OPTIONS title = Production Simulation cpp = /lib/cpp define = -DPOSRES_DNA ; RUN CONTROL PARAMETERS integrator = md tinit = 0 ; Starting time dt = 0.0005 ; 2 femtosecond time step for integration nsteps = 100000000 ; OUTPUT CONTROL OPTIONS nstxout = 50000 ; Writing full precision coordinates every nanosecond nstvout = 50000 ; Writing velocities every nanosecond nstfout = 0 ; Not writing forces nstlog = 5000 ; Writing to the log file every step nstenergy = 5000 ; Writing out energy information every step nstxtcout = 5000 ; Writing coordinates every 5 ps energygrps = Protein DNA water_and_ions ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist = 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 78 epsilon_r = 1 vdw-type = Cut-off rvdw = 1.4 ; Temperature coupling Tcoupl = Berendsen tc-grps = Protein DNA water_and_ions tau_t = 0.1 0.1 0.1 ref_t = 200 200 200 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 Thanks for your help, Matthias -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
