Hi justin,<div> thank you for reply,</div><div>1. I sort out the specific time pdb ..</div><div> I notice the folllowing things.. </div><div> 26 and 111 are the atoms of two different protein ..</div>
<div> one is on the right hand side near the box boundary ..and other is protruding from the <br> left hand side box boundary ,so they may close to each other enough ..</div><div> so is the simulation is wrong or right ...</div>
<div><br></div><div>2. Please could you tell me , What are the right parameter for the G96 53a6 force field ??</div><div><br></div><div>thank you a lot for help ..</div><div><br><div class="gmail_quote">On Thu, Mar 29, 2012 at 7:03 PM, rama david <span dir="ltr"><<a href="mailto:ramadavidgroup@gmail.com">ramadavidgroup@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Gromacs friends,<div> Thank you justin for your explaination ..</div><div><br></div><div>It is, however, common to compromise</div>
<div>in this respect, and make the solvent layer somewhat smaller in order to reduce the computational</div>
<div>cost. For efficiency reasons the cut-off with triclinic boxes is more restricted. For grid search the</div><div>extra restriction is weak:</div><div><br></div><div>Rc < min(ax; by; cz) (3.5)</div><div><br></div><div>
For simple search the extra restriction is stronger:</div><div><br></div><div>Rc <1/2min(ax; by; cz) (3.6) </div><div><br></div><div>So from manual and your answer , should I conclude that -d 1.0 nm distance is sufficient ???</div>
<div><br></div><div>if I using command genbox ..... -ci -nmol ... , the molecule are going to put randomly ..</div><div>In that case how to maintain -d .. ??? </div><div>I am in these confusion because of following reason ..... </div>
<div><br></div><div>I am try to put max molecule to study there interaction ...</div>
<div><br></div><div><span> I run simulation of 4 same molecule keep apart in box </span><br><span>of 4 4 4 dimension ..( 71 atom in one molecule = 71 * 4 = total atom are 284 )</span><br><span>force field = gromacs96 53a6</span><br>
<br><span>COM (center of mass) information of molecules</span><br><span>system size : 1.255 1.577 1.883 </span><br><span>box vectors : 4.000 4.000 4.000 (nm)</span><br><span> mol1 : 2.057 0.844 0.744</span><br>
<span> mol 2 : 2.057 0.844 3.141</span><br><span> mol 3 : 2.057 3.244 0.744</span><br><span> mol 4 : 2.057 3.244 3.141</span><br><br><span>(Four molecule are kept at the four corner of square</span><br>
<span> of each side 2.4 nm</span><br><span> four molecule are catenated in same pdb )</span><br><br><span> my md.mdp input is like the ..</span><br><br><span>;Neighborsearching</span><br>
<span>ns_type = grid ; search neighboring grid cells</span><br><span>nstlist = 5 ; 10 fs</span><br><span>rlist = 1.0 ; short-range neighborlist cutoff (in nm)</span><br>
<span>rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)</span><br><span>rvdw = 1.0 ; short-range van der Waals cutoff (in nm)</span><br><span>; Electrostatics</span><br>
<span>coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics</span><br><span>pme_order = 4 ; cubic interpolation</span><br><span>fourierspacing = 0.16 ; grid spacing for FFT</span><br>
<span> </span><br><span>With command g_mindist -pi </span></div><div><span> , select option - 1 (Protein )</span></div><div>In the index file protein contain information on protein ...<br>
<span>I got the following result.. </span><br><br><span>The shortest periodic distance is 0.141718 (nm) at time 7692 (ps),</span><br><span>between atoms 26 and 111</span><br><br>
<span>Is the simulation is behaving abnormal(I.e simulation is wrong ) or I</span><br><span> have to select the option system on prompting ??? I am very new to these simulation field.. </span><br>
<span>so all suggestion are appreciable ...</span>
</div><div class="HOEnZb"><div class="h5"><div><br></div><div> <br><br><div class="gmail_quote">On Thu, Mar 29, 2012 at 5:05 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
rama david wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>
Hi Gromacs users ,<br>
as per the link given on gromacs website...<br></div>
Introduction to Molecular Dynamics Simulations and Analysis <<a href="http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/" target="_blank">http://nmr.chem.uu.nl/%<u></u>7Etsjerk/course/molmod/</a>> - 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).<div>
<br>
<br>
<br>
editconf -f protein-EM-vacuum.pdb -o protein-PBC.gro -bt dodecahedron -d 1.0<br>
<br>
mdp file parameter are as follow ,<br>
<br>
coulombtype = Reaction-Field<br>
rcoulomb = 1.4<br>
epsilon_rf = 78<br>
epsilon_r = 1<br>
vdw-type = Cut-off<br>
rvdw = 1.4<br>
so my query is ..<br>
<br>
As mention in manual ...<br>
(Page no 14 manual 4.5.4 I am using the Gromacs 4.5.4 )<br></div>
*This means that the length of each box vector must exceed the length of the macromolecule in the<br>
direction of that edge plus two times the cut-off radius Rc *.<br>
</blockquote>
<br>
Read the next sentence in the manual.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
/In the tutorial -d 1.0 is less than 1.4 ./..<div><br>
I noticed that manual version and tutorial gromacs version are different ...<br>
But it raise a lot of confusion for new users like me..<br>
1. Is the -d .. should be equal or more than cutt off ???<br>
or<br>
Is the -d .. should be equal or more than cutt-off??<br>
<br>
</div></blockquote>
<br>
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: <a href="http://lists.gromacs.org/pipermail/gmx-users/2012-March/069617.html" target="_blank">http://lists.gromacs.org/<u></u>pipermail/gmx-users/2012-<u></u>March/069617.html</a><br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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