[gmx-users] About periodic image of system.......

[rama david]

Dear expert,

I am simulating the protein-ligand system.

Mdp file parameter are

 Neighborsearching
ns_type         = grid          ; search neighboring grid cells
nstlist         = 5             ; 10 fs
rlist           = 0.9           ; short-range neighborlist cutoff (in nm)
rcoulomb        = 0.9           ; short-range electrostatic cutoff (in nm)
vdw-type        = Cut-off
rvdw            = 1.4           ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype     = PME           ; Particle Mesh Ewald for long-range
electrostatics
pme_order       = 4             ; cubic interpolation



 the command line and out-put is shown for box preparation are as follow

editconf_mpi -f process.pdb -o princ.pdb -box 11.4  10.7  10.7 -princ -c

new system size :  8.576  4.832  4.220
    shift       :  5.003  5.426  6.257 (nm)
new center      :  5.700  5.350  5.350 (nm)
new box vectors : 11.400 10.700 10.700 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  :1305.19               (nm^3)

I put the 40 ns production run.


When I checked the pbc by command


 g_mindist_mpi -od pbc-1.xvg -w -pi  -s md.tpr -f md.xtc -b 12000

I got the following result..
The shortest periodic distance is 0.154938 (nm) at time 16162 (ps),
between atoms 223 and 3270

 Atom 223 is protein chain A atom and 3270 is chain B ( ligand atom) .

 I process on xtc file by -pbc nojump and got the nojump.xtc file

I  run the above g_mindist_mpi command on these XTC file . I get

The shortest periodic distance is 3.39417 (nm) at time 12350 (ps),
between atoms 2706 and 3241





So is my system is seeing its periodic image..and I have to rerun..???

(The box  i  used in simulation is  larger than -d 1.0 )

Am I making mistake in comand line???

All suggestion are welcome .


With best wishes and regards,

Rama david.