Hi Mark,<div><br></div><div>Yes i checked the procedure on the original structure. It woks fine. As for genconf i used the following</div><div><br></div><div>genconf -f dppc128.pdb -o out.gro -nbox 2 2 1 </div><div><br></div>
<div>As Justin pointed out, I did not correct the periodicity of original structure before using genconf .</div><div><br></div><div>Thank you,</div><div>Amit<br><br><div class="gmail_quote">On Fri, Oct 9, 2009 at 5:44 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">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>
</blockquote>
<br></div>
What command line did you use?<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>
</blockquote>
<br></div>
Test your protocol on the original coordinate file. It needs to work for your procedure to be sound.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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>
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>
Same warnings were printed out during energy minimization.<br>
</blockquote>
<br></div>
You don't have periodic molecules. Changing mdp options haphazardly is a recipe for problems. Read 7.3 about them in the first instance, and then look up in the table of contents for more background.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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>
</blockquote>
<br></div>
Yup, bad idea. Fix the underlying problem, not the symptoms.<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
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