Hi Justin,<div><br></div><div>Yes you are right. I didnt fix the periodicity to start with. Could you tell me how to do that, which command to work with?</div><div>Thanks.</div><div><br></div><div>amit<br><br><div class="gmail_quote">
On Fri, Oct 9, 2009 at 5:39 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">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;">
<div class="im"><br>
<br>
Amit Choubey wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gromacs Users,<br>
<br>
I have been trying to generate a larger lipid system but am running into troubles due to improper initial co-ordinates set up. Following are the steps i am trying to follow.<br>
<br>
1. I start with a 128 dppc membrane and use genconf to create a larger system. I got the dppc128.pdb from Dr. Peter Tieleman's website.<br>
<br>
</blockquote>
<br></div>
Did you correct for periodicity before you extended the system? The files distributed by Tieleman are compact representations.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
2. I changed my topology file accordingly (change the number of DPPC and Water molecules)<br>
<br>
3. I move on to energy minimization. During the mdrun i see the following message :-<br>
<br>
Warning: 1-4 interaction between 1854 and 1857 at distance 6.249 which is larger than the 1-4 table size 2.800 nm<br>
These are ignored for the rest of the simulation<br>
This usually means your system is exploding,<br>
if not, you should increase table-extension in your mdp file<br>
or with user tables increase the table size<br>
<br>
</blockquote>
<br></div>
Looks to me like two bonded atoms are across the box from each other, which seems to answer my question above :)<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I also notice that the max force does not converge to less than 2000 rather its of the order of 2e+06 .<br>
<br>
4. I tried to do energy minimization again on the above system but the steepest descent could not change the potential energy substantially and terminated after less that 20 steps. I again noticed the following warning <br>
Warning: 1-4 interaction between 1854 and 1857 at distance 5.269 which is larger than the 1-4 table size 2.800 nm<br>
These are ignored for the rest of the simulation<br>
This usually means your system is exploding,<br>
if not, you should increase table-extension in your mdp file<br>
or with user tables increase the table size<br>
<br>
5. Now i changed my mdp files to do periodic_molecules = yes . Note pbc = xyz has been used as default.<br>
<br>
</blockquote>
<br></div>
Bad idea. This option is for "infinite" molecules, like nanotubes or graphene sheets that are supposed to extend across the simulation box.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Same warnings were printed out during energy minimization.<br>
<br>
6. I also tried to use the table-extension option and increased its value to 10 nm but later the LINCS printed out too many warnings and MD could not be done. I know that its not at all a good idea to increase the 1-4 cut off.<br>
<br>
</blockquote>
<br></div>
The standard advice is to fix the problem with the system, not change the table-extension.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
By the way to be specific the system size was 12 x 12 x 6 in nm3. I had 256 lipids and about 7300 water molecules.<br>
<br>
I believe that this might not be the best way to create a larger bilayer system. Could somebody suggest me other ways of doing this?<br>
<br>
</blockquote>
<br></div>
Fix periodicity, then use genconf.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Any help will be appreciated thank you<br>
<br>
Amit<br>
<br>
<br>
<br></div>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<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.vt.edu/Pages/Personal/justin</a><br>
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