On 11/10/12 5:42 AM, rama david wrote:
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
You shouldn't use -b here. You should be checking the entire trajectory for
problems.
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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
