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

[rama david]

Hi justin ,
Thank you for reply.
Mdp parameters are as follow ,

; 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)

I choose the protein for g_mindist option..

Please could you explain me what am getting and why it is not violation of
pbc????

Sorry for these basic question, but I am confuse with these result


With best wishes and regards,
Rama david.

On Sat, Nov 10, 2012 at 6:55 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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