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
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