Re: [gmx-users] about g_mindist....

2012-03-29 Thread Mark Abraham 

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 > 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  : 2.0570.844  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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Re: [gmx-users] about g_mindist....

2012-03-29 Thread 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 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  : 2.0570.844  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 listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
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Please search the archive at 
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Re: [gmx-users] about g_mindist....

2012-03-29 Thread Mark Abraham 

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  : 2.0570.844  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 listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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[gmx-users] about g_mindist....

2012-03-29 Thread rama david 
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  : 2.0570.844  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)

 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 ...
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists