Thanks for your mail sir. I will do some reading as per your suggestion. On Thu, Apr 9, 2009 at 10:45 AM, <[email protected]> wrote:
> Dear Pawan, > > 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. > > 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. > > 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" ;) > > Chris. > > > > -- original message -- > > Hello Mark Sir, > > I have tried that way also. > The command i used was grompp -f pr.mdp -n index.ndx -c box_em.pdb -p > topol.top -o box_pr.tpr > But this time i get an error like this "Atom 1 defined in multiple groups > (1 > & 3). " > How to overcome this error ? > > Thanking you, > Pawan > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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