rama david 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)

These settings are not correct for Gromos96 53a6.

; 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


Identify what atoms 26 and 111 are. If they are part of the same molecule, then yes, you have a problem. It sounds to me like you have 4 separate molecules, and 2 of them are at a very short distance in the starting configuration. This is not the same situation as when a molecule sees itself. Whether or not this is what you want for your simulation setup is up to you.

-Justin

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 <jalem...@vt.edu <mailto:jalem...@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 <http://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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--
========================================

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

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