[gmx-users] about g_mindist....

[Mark Abraham]

On 29/03/2012 7:20 PM, rama david wrote:
> 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    )

No they're not starting on a square. Look at those z coordinates above.

>
>  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 ...

Shrug. You've measured the inter-group distance between a group and 
itself. Curiously enough, that's the length of a C-C bond, or similar. 
g_mindist -h is required reading. Also, we don't even know what's in 
group Protein, or your g_mindist command line.

Mark