[gmx-users] about g_mindist....

[rama david]

Hi everybody ,
             I run simulation of 4 same  molecule keep apart in box
of 4 4 4 dimension ..( 71 atom in one molecule = 71 * 4 = total atom are
284 )
force field = gromacs96   53a6

COM (center of mass) infirmation of molecules
system size :  1.255  1.577  1.883
box vectors :  4.000   4.000   4.000 (nm)
 mol1          : 2.057    0.844  1.941
 mol 2          :  2.057  0.844  3.141
 mol 3          : 2.057   3.244   0.744
 mol 4          : 2.057   3.244   3.141

(Four molecule are kept at the four corner of square
 of each side 2.4 nm
    four molecule are catenated in same pdb    )

 my md.mdp input is like the ..

;Neighborsearching
ns_type        = grid        ; search neighboring grid cells
nstlist        = 5        ; 10 fs
rlist        = 1.0        ; short-range neighborlist cutoff (in nm)
rcoulomb    = 1.0        ; short-range electrostatic cutoff (in nm)
rvdw        = 1.0        ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype    = PME        ; Particle Mesh Ewald for long-range
electrostatics
pme_order    = 4        ; cubic interpolation
fourierspacing    = 0.16        ; grid spacing for FFT

With  command  g_mindist , select option - 1 (Protein )
I got the following result..

The shortest periodic distance is 0.141718 (nm) at time 7692 (ps),
between atoms 26 and 111

Is the simulation is behaving abnormal(I.e  simulation is wrong ) or  I
 have to select the option system on prompting ??? I am very new to these
simulation field..
so all suggestion are appreciable ...
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