[gmx-users] about g_mindist....
Mark.Abraham at anu.edu.au
Thu Mar 29 10:32:59 CEST 2012
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 ..
> 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
> 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.
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