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On 30/03/2012 12:40 AM, rama david wrote:
<blockquote
cite="mid:CAD=-SYEN0DuaPoPDCev1e1d7Ltckpp7ES_V7vaYE9a31uezmMw@mail.gmail.com"
type="cite">Hi mark ..
<div>thank you for your suggestion..</div>
<div>My command line is g_mindist -f ..xtc -s ..tpr -od
minimal.xvg -pi </div>
<div> protein group contain information about the 284 atom (i.e.
All protein atoms)</div>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAD=-SYEN0DuaPoPDCev1e1d7Ltckpp7ES_V7vaYE9a31uezmMw@mail.gmail.com"
type="cite">
<div>..</div>
<div>So please suggest me the right way ..</div>
<div><br>
<div class="gmail_quote">On Thu, Mar 29, 2012 at 2:02 PM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">On 29/03/2012 7:20 PM, rama david wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi everybody ,<br>
I run simulation of 4 same molecule keep
apart in box<br>
of 4 4 4 dimension ..( 71 atom in one molecule = 71 * 4
= total atom are 284 )<br>
force field = gromacs96 53a6<br>
<br>
COM (center of mass) infirmation of molecules<br>
system size : 1.255 1.577 1.883<br>
box vectors : 4.000 4.000 4.000 (nm)<br>
mol1 : 2.057 0.844 1.941<br>
mol 2 : 2.057 0.844 3.141<br>
mol 3 : 2.057 3.244 0.744<br>
mol 4 : 2.057 3.244 3.141<br>
<br>
(Four molecule are kept at the four corner of square<br>
of each side 2.4 nm<br>
four molecule are catenated in same pdb )<br>
</blockquote>
<br>
</div>
No they're not starting on a square. Look at those z
coordinates above.
<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
my md.mdp input is like the ..<br>
<br>
;Neighborsearching<br>
ns_type = grid ; search neighboring grid
cells<br>
nstlist = 5 ; 10 fs<br>
rlist = 1.0 ; short-range neighborlist
cutoff (in nm)<br>
rcoulomb = 1.0 ; short-range electrostatic
cutoff (in nm)<br>
rvdw = 1.0 ; short-range van der Waals
cutoff (in nm)<br>
; Electrostatics<br>
coulombtype = PME ; Particle Mesh Ewald for
long-range electrostatics<br>
pme_order = 4 ; cubic interpolation<br>
fourierspacing = 0.16 ; grid spacing for FFT<br>
<br>
With command g_mindist , select option - 1 (Protein )<br>
I got the following result..<br>
<br>
The shortest periodic distance is 0.141718 (nm) at time
7692 (ps),<br>
between atoms 26 and 111<br>
<br>
Is the simulation is behaving abnormal(I.e simulation
is wrong ) or I<br>
have to select the option system on prompting ??? I am
very new to these simulation field..<br>
so all suggestion are appreciable ...<br>
</blockquote>
<br>
</div>
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.<span class="HOEnZb"><font
color="#888888"><br>
<br>
Mark<br>
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