[gmx-users] About cutt-off scheme ..

rama david ramadavidgroup at gmail.com
Thu Mar 29 16:05:11 CEST 2012 

Hi justin,
             thank you for reply,
1.    I sort out the specific time pdb ..
     I notice the folllowing things..
     26 and 111 are the atoms of two different protein ..
     one is  on the right hand side near the box boundary ..and other is
protruding from the
     left hand side box boundary ,so they may close to each other enough ..
     so is the simulation is wrong or right ...

2.   Please could you tell me , What are the right parameter for the G96
53a6 force field ??

thank you a lot for help ..

On Thu, Mar 29, 2012 at 7:03 PM, rama david <ramadavidgroup at gmail.com>wrote:

> Hi Gromacs friends,
>   Thank you justin for your explaination ..
>
> It is, however, common to compromise
> in this respect, and make the solvent layer somewhat smaller in order to
> reduce the computational
> cost. For efficiency reasons the cut-off with triclinic boxes is more
> restricted. For grid search the
> extra restriction is weak:
>
> Rc < min(ax; by; cz) (3.5)
>
> For simple search the extra restriction is stronger:
>
> Rc <1/2min(ax; by; cz) (3.6)
>
> So from manual and your answer , should I conclude that -d 1.0 nm distance
> is sufficient  ???
>
> if I using command genbox ..... -ci  -nmol ... , the molecule are going to
> put randomly ..
> In that case how to maintain  -d  .. ???
> I am in these confusion because of following reason .....
>
> I am try to put max molecule to study there interaction ...
>
>      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) information of molecules
> system size :  1.255  1.577  1.883
> box vectors :  4.000   4.000   4.000 (nm)
>  mol1          : 2.057    0.844  0.744
>  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    -pi
>  , select option - 1 (Protein )
> In the index file protein contain information on 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 ...
>
>
>
> On Thu, Mar 29, 2012 at 5:05 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> rama david wrote:
>>
>>> Hi Gromacs users ,
>>> as per the link given on gromacs website...
>>> Introduction to Molecular Dynamics Simulations and Analysis <
>>> http://nmr.chem.uu.nl/%**7Etsjerk/course/molmod/<http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/>>
>>> - Tutorial for performing and analyzing simulations of proteins. Includes
>>> examples of many of the gromacs analysis tools and addresses a number of
>>> issues that are commonly raised on the GROMACS user list. This tutorial
>>> uses GROMACS version 3.3.1 (Tsjerk A. Wassenaar).
>>>
>>>
>>>
>>> editconf -f protein-EM-vacuum.pdb -o protein-PBC.gro -bt dodecahedron -d
>>> 1.0
>>>
>>> mdp file parameter are as follow ,
>>>
>>> coulombtype              = Reaction-Field
>>> rcoulomb                 = 1.4
>>> epsilon_rf               = 78
>>> epsilon_r                = 1
>>> vdw-type                 = Cut-off
>>> rvdw                     = 1.4
>>>  so my query  is ..
>>>
>>> As mention in manual ...
>>> (Page no 14  manual 4.5.4  I am using the Gromacs 4.5.4  )
>>> *This means that the length of each box vector must exceed the length of
>>> the macromolecule in the
>>> direction of that edge plus two times the cut-off radius Rc *.
>>>
>>
>> Read the next sentence in the manual.
>>
>>     /In  the tutorial  -d 1.0  is less than 1.4  ./..
>>>
>>>  I noticed that manual version and tutorial  gromacs version are
>>> different ...
>>> But it raise a lot of confusion  for new users like me..
>>>  1. Is the -d .. should be equal  or more than cutt off ???
>>>             or
>>>  Is the -d   .. should be equal or more than cutt-off??
>>>
>>>
>> The basic point is that in all simulations you have to avoid the same
>> molecule "seeing" itself across a periodic boundary.  So in reality, you
>> need a periodic distance (which is equivalent to the value set with -d,
>> times 2) that exceeds the longest cutoff.  Assuming the unit cell does not
>> undergo massive shrinking, this value is generally pretty stable in an
>> aqueous environment.  Setting -d 1.0 is common because it creates a 2.0-nm
>> distance between a centered solute, which exceeds your cutoff and is
>> sufficient to avoid the influence of water ordering, as discussed recently:
>> http://lists.gromacs.org/**pipermail/gmx-users/2012-**March/069617.html<http://lists.gromacs.org/pipermail/gmx-users/2012-March/069617.html>
>>
>> -Justin
>>
>> --
>> ==============================**==========
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
>> --
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>
>
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