[gmx-users] Constant-Force Pulling of Ubiquitin

[XAvier Periole]

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
> 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
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