[gmx-users] about g_mindist....
ramadavidgroup at gmail.com
Thu Mar 29 15:40:03 CEST 2012
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
So please suggest me the right way ..
On Thu, Mar 29, 2012 at 2:02 PM, Mark Abraham <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 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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