[gmx-users] Re: Membrane protein tutoria

Pawan Kumar pawan.chinari at gmail.com
Thu Apr 9 07:21:53 CEST 2009

Thanks for your mail sir.
I will do some reading as per your suggestion.

On Thu, Apr 9, 2009 at 10:45 AM, <chris.neale at utoronto.ca> 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
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