You want to switch to sd instead of md.
> On Oct 29, 2013, at 17:43, Vivian <ww...@bu.edu> wrote: > > Hi GMX Users, > > I am using Gromacs (Version 4.5.5) to do constant-force pulling of ubiquitin > and it's a implicit model. My mdp file for pulling is shown as following. > > integrator = md > dt = 0.001 ; ps ! > nsteps = 500000 ; total 500 ps. > > nstxout = 100 > nstvout = 100 > nstfout = 100 > nstlist = 10 > nstlog = 100 > nstcalcenergy =100 > > rlist = 5 > rvdw = 5 > rcoulomb = 5 > coulombtype = cut-off > vdwtype = cut-off > table-extension = 5 > bd_fric = 0 > ld_seed = -1 > pbc = no > ns_type = simple > constraints = all-bonds > lincs_order = 4 > lincs_iter = 1 > lincs-warnangle = 30 > > Tcoupl = v-rescale > tau_t = 1.0 > tc-grps = Protein > ref_t = 300 > > Pcoupl = no > > gen_vel = yes > gen_temp = 300 > gen_seed = 173529 > > comm_mode = Angular > nstcomm =100 > > > ; IMPLICIT SOLVENT ALGORITHM > implicit_solvent = gbsa > > ; GENERALIZED BORN ELECTROSTATICS > ; Algorithm for calculating Born radii > gb_algorithm = Still > ; Frequency of calculating the Born radii inside rlist > nstgbradii = 1 > ; Cutoff for Born radii calculation; the contribution from atoms > ; between rlist and rgbradii is updated every nstlist steps > rgbradii = 5 > ; Dielectric coefficient of the implicit solvent > gb_epsilon_solvent = 80 > ; Salt concentration in M for Generalized Born models > gb_saltconc = 0 > ; Scaling factors used in the OBC GB model. Default values are OBC(II) > gb_obc_alpha = 1 > gb_obc_beta = 0.8 > gb_obc_gamma = 4.85 > gb_dielectric_offset = 0.009 > sa_algorithm = Ace-approximation > ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA > ; The value -1 will set default value for Still/HCT/OBC GB-models. > sa_surface_tension = 2.05016 > > ; Pull code > pull = constant_force > ;Center of mass pulling using a linear potential and therefore a constant > force. > pull_geometry = direction > pull_start = yes ; define initial COM distance > 0 > pull_ngroups = 1 > pull_group1 = Chain_B > pull_group0 = Chain_A > pull_k1 = -500 ; kJ mol^-1 nm^-2 > pull_vec1 = 0.0 0.0 1.0 > > However, after pulling simulation, it turns out the potential of this system > becomes lower rather than higher (from -10000 to -20000). It's very wired > since potential should become larger after pulling. > Here is the notification after g_energy: > > Energy Average Err.Est. RMSD Tot-Drift > ------------------------------------------------------------------------------- > > Potential -20734.5 230 1268.47 -1385.71 > (kJ/mol) > > You may want to use the -driftcorr flag in order to correct for spurious > drift in the graphs. Note that this is not > a substitute for proper equilibration and sampling! You should select the > temperature in order to obtain fluctuation properties. > > I wonder whether there is any problem with my mdp file. > Thank you so much!! > > Best, > Vivian > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Constant-Force-Pulling-of-Ubiquitin-tp5012065.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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
