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>
<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 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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</font></span></blockquote></div><br></div>