[gmx-users] COM-Pulling-Non linearity of pulled group

[Haidy Metwally]

Hello,


I tried to do COM-pulling simulation (using Gromacs 5 .0.4) to pull a molecule  away from sodium ion that is bound to acidic site of protein. My reference group is protein backbone. I do that in presence of solvent. The main problem is that my pulled group is not pulled in linear fashion, it rotates around the solvent droplet so  when it is being pulled it shuffle around in different directions.  This happens even if I changed the pull-geometry to direction using a vector. Also, I tried to change the pull -dimension from YYY to NNY and the movement was not in z- direction.    The only way I can get rid of that rotation or shuffling around is do my pulling without solvent and I need to see the pulling effect in the presence of solvent. I wonder if there is a possibility that my reference group is moving in the solvent and so the spring moves with it,although the reference is supposed to be fixed.


Can anyone help me in that?


Any suggestions will be appreciated


Here is a copy of my .mdp file
title       = Umbrella pulling simulation
define      = -DPOSRES_Protein

; Run parameters
integrator  = md
dt          = 0.002
tinit       = 0
nsteps      = 250000    ; 500 ps
nstcomm     = 10
; Output parameters
nstxout     = 5000      ; every 10 ps
nstvout     = 5000
nstfout     = 500
nstxtcout   = 500       ; every 1 ps
nstenergy   = 500
; Bond parameters
constraint_algorithm    = lincs
constraints             = all-bonds
continuation            = yes       ; continuing from md run
; Single-range cutoff scheme
nstlist     = 50
ns_type     = simple
cutoff-scheme   =  verlet
comm_mode     =  linear
coulombtype     =  cut-off
vdwtype             =  cut-off
rlist                      = 333.3
rcoulomb            = 333.3
rvdw                    = 333.3
Tcoupl                = nose-hoover
ref_t                    = 370
tau_t                   = 0.5
tc-grps                = system
nsttcouple          = 1
;Pressure coupling
Pcoupl              = NO
;Generate velocities is off
gen_vel     = no
; Periodic boundary conditions are on in all directions
pbc     = xyz
; Pull code
pull                    = umbrella
pull_geometry       = distance      ; simple distance increase
pull_dim                   = Y Y Y
pull_start                   = yes           ; define initial COM distance > 0
pull_ngroups             = 2
pull_ncoords                  = 1
pull_group1_name        = X                     ;its is called like that in index file
pull_group2_name        = Backbone
pull_coord1_groups      = 1 2
pull_coord1_rate        = 0.02          ;
pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2


Thanks alot

Best Regards,

Haidy Metwally

PhD. Candidate