Dear GMX users
I used charmm36 force field to run MD simulation on my receptor and ligand 
which has 2 phosphotyrosine groups. All of steps that I did are following as:

1) gmx pdb2gmx -f .pdb -o .gro -water tip4p -ignh -his2) gmx editconf -f .gro 
-o newbox.gro -c -d 1.0 -bt dodecahedron3)gmx solvate -cp newbox.gro -cs 
tip4p.gro -p .top -o .gro 4) gmx grompp -f ions.mdp -c .gro -p .top -o 
ions.tpr5) gmx genion -s ions.tpr -o .gro -p .top -pname NA -np 11 -nname CL6) 
gmx frompp -f minim.mdp -c .gro -p .top -o em.tpr7) gmx mdrun -v -deffnm em
ions.mdp and minim.mdp files:; minim.mdp - used as input into grompp to 
generate em.tpr
integrator    = steep        ; Algorithm (steep = steepest descent minimization)
emtol        = 1000.0      ; Stop minimization when the maximum force < 1000.0 
kJ/mol/nm
emstep      = 0.01      ; Energy step size
nsteps        = 50000          ; Maximum number of (minimization) steps to 
perform

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist            = 1            ; Frequency to update the neighbor list and 
long range forces
cutoff-scheme   = Verlet
ns_type            = grid        ; Method to determine neighbor list (simple, 
grid)
coulombtype        = PME        ; Treatment of long range electrostatic 
interactions
rcoulomb        = 1.2        ; Short-range electrostatic cut-off
rvdw            = 1.2        ; Short-range Van der Waals cut-off
vdwtype         = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
pbc                = xyz         ; Periodic Boundary Conditions (yes/no)
DispCorr = no

then I checked em.gro using vmd, the ligand was in the active site and there 
was no problem.
8) gmx grompp -f nvt.mdp -c em.gro -p .top -o nvt.tpr9) gmx mdrun -deffnm nvt
nvt.mdp file:
title        = CHARMM36 EGFR NVT equilibration 
define        =  -DUSE_OLD_C3
; Run parameters
integrator    = md        ; leap-frog integrator
nsteps        = 200000        ; 2 * 50000 = 400 ps
dt            = 0.002        ; 2 fs
; Output control
nstxout        = 500        ; save coordinates every 1.0 ps
nstvout        = 500        ; save velocities every 1.0 ps
nstenergy    = 500        ; save energies every 1.0 ps
nstlog        = 500        ; update log file every 1.0 ps
; Bond parameters
continuation            = no        ; first dynamics run
constraint_algorithm    = lincs        ; holonomic constraints 
constraints                = h-bonds    ; all bonds (even heavy atom-H bonds) 
constrained
lincs_iter                = 1            ; accuracy of LINCS
lincs_order                = 4            ; also related to accuracy
; Neighborsearching
cutoff-scheme   = Verlet
ns_type            = grid        ; search neighboring grid cells
nstlist            = 10        ; 20 fs, largely irrelevant with Verlet
rcoulomb        = 1.2        ; short-range electrostatic cutoff (in nm)
rvdw            = 1.2        ; short-range van der Waals cutoff (in nm)
vdwtype = cutoff
vdw-modifier = force-switch
rlist = 1.2
rvdw-switch = 1.0
; Electrostatics
coulombtype        = PME    ; Particle Mesh Ewald for long-range electrostatics
pme_order        = 4        ; cubic interpolation
fourierspacing    = 0.16    ; grid spacing for FFT
; Temperature coupling is on
tcoupl        = V-rescale                ; modified Berendsen thermostat
tc-grps        = Protein Non-Protein    ; two coupling groups - more accurate
tau_t        = 0.1      0.1           ; time constant, in ps
ref_t        = 300       300           ; reference temperature, one for each 
group, in K
; Pressure coupling is off
pcoupl        = no         ; no pressure coupling in NVT
; Periodic boundary conditions
pbc        = xyz            ; 3-D PBC
; Dispersion correction
DispCorr    = no        ; account for cut-off vdW scheme
; Velocity generation
gen_vel        = yes        ; assign velocities from Maxwell distribution
gen_temp    = 300        ; temperature for Maxwell distribution
gen_seed    = -1        ; generate a random seed
but when I checked nvt.gro by VMD ,  viewed  the receptor and ligand went out 
of the box, almost completely and ligand was separated from the protein, 
completely. Is there anyone who can help me and advice me why it was happened?
best Farial
 



 
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Reply via email to