On 30/03/2012 12:40 AM, rama david wrote:
Hi mark ..
thank you for your suggestion..
My command line is g_mindist -f ..xtc -s ..tpr -od minimal.xvg -pi
protein group contain information about the 284 atom (i.e. All
protein atoms)
So clearly some part of some molecule is protruding across periodic
boundaries, since the nearest distance between any periodic image of any
atom to any original atom is so small. Since your initial structure
isn't in the square arrangement you think it is in, I suggest you go
back and set up your system better.
Mark
..
So please suggest me the right way ..
On Thu, Mar 29, 2012 at 2:02 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
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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