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

[Justin Lemkul]

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

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