[gmx-users] Re: Membrane protein tutoria

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Apr 9 07:15:22 CEST 2009

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" ;)


-- 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,

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