[gmx-users] Constant-Force Pulling of Ubiquitin

[Vivian]

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

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