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 -- 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
