[gmx-users] about g_mindist....
Mark.Abraham at anu.edu.au
Thu Mar 29 17:55:00 CEST 2012
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.
> So please suggest me the right way ..
> On Thu, Mar 29, 2012 at 2:02 PM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at 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
> 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 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.
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