[gmx-users] About periodic image of system.......
jalemkul at vt.edu
Sat Nov 10 14:25:21 CET 2012
On 11/10/12 5:42 AM, rama david wrote:
> Dear expert,
> 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)
> ; Electrostatics
> 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
You shouldn't use -b here. You should be checking the entire trajectory for
> 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) .
What group did you choose for analysis, System? This is not a problem. PBC
artifacts only arise when a molecule sees itself.
> 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
This also looks fine, given the cutoffs described above, even without knowing
what these atoms are.
> So is my system is seeing its periodic image..and I have to rerun..???
I see no evidence of a problem.
> (The box i used in simulation is larger than -d 1.0 )
> Am I making mistake in comand line???
Aside from what's noted above, no.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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