[gmx-users] About periodic image of system.......
ramadavidgroup at gmail.com
Sat Nov 10 11:42:04 CET 2012
I am simulating the protein-ligand system.
Mdp file parameter are
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)
coulombtype = PME ; Particle Mesh Ewald for long-range
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,
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