rama david wrote:
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 ...
This seems fine. The point of the minimum image convention is that one should
not allow the same molecule to double-count interactions due to periodicity.
Two different molecules interacting is not a big deal, that's just what happens
across PBC.
If you have 4 proteins, each at the "corner" of the box (which is irrelevant due
to PBC), it's the same as having all four clustered in the "center" of the box
to begin with. Use a periodic representation in VMD (or whatever you like) to
see what I mean.
2. Please could you tell me , What are the right parameter for the G96
53a6 force field ??
With PME, you would use:
rlist = 0.9
rcoulomb = 0.9
rvdw = 1.4
-Justin
thank you a lot for help ..
On Thu, Mar 29, 2012 at 7:03 PM, rama david <ramadavidgr...@gmail.com
<mailto:ramadavidgr...@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 <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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