[gmx-users] Constant-Force Pulling of Ubiquitin
x.periole at rug.nl
Tue Oct 29 20:27:16 CET 2013
You want to switch to sd instead of md.
> On Oct 29, 2013, at 17:43, Vivian <wwtao at 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
> 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
> 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!!
> 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.
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