Thanks for your mail sir.<br>I will do some reading as per your suggestion.<br><br><div class="gmail_quote">On Thu, Apr 9, 2009 at 10:45 AM, <span dir="ltr"><<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Dear Pawan,<br>
<br>
I suggest that you try doing some protein in water simulations or some available tutorials before you proceed with your bilayer study. You might also consider reading the error messages more carefully and attempting to troubleshoot based on these messages. If the error message is "popc not defined in the index file" or "Atom 1 defined in multiple groups (1 & 3)" then I think that you already have the information that you need. At least in the second case you have at least as much information as we do -- one might ask why you can't have an atom in multiple groups, and I'll hint that this is not an .ndx file problem in and of itself.<br>
<br>
I hope that this comes across as I intend since I'm only trying to be helpful to you here. Bilayer simulations are not nearly as simple as those with proteins in water and if you don't understand the role of the .ndx file then your time might be better spent reading the manual and running some simpler simulations. Why do I say this? Mostly because there is no error given for "your bilayer has entered the gel phase" or "your temperature coupling of a group with too few atoms has lead to incorrect results" and it is thus useful to be clear what is going on before you decide what to do since you can still do things incorrectly without getting an error message.<br>
<br>
Further, I would prefer if you pick some more useful subject lines. This has nothing to do with the membrane protein tutorial that Justin recently provided. At least there is no more "doubt about membrane simulation" ;)<br>
<br>
Chris.<br>
<br>
<br>
<br>
-- original message --<br>
<br>
Hello Mark Sir,<br>
<br>
I have tried that way also.<br>
The command i used was grompp -f pr.mdp -n index.ndx -c box_em.pdb -p<br>
topol.top -o box_pr.tpr<br>
But this time i get an error like this "Atom 1 defined in multiple groups (1<br>
& 3). "<br>
How to overcome this error ?<br>
<br>
Thanking you,<br>
Pawan<br>
<br>
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</blockquote></div><br>