[gmx-users] about g_mindist....

[rama david]

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 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 ..
>>
>> ;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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120329/f43cf198/attachment.html>