[gmx-users] RE:RE: bicelle modeling using CG MODEL

Mark Abraham Mark.Abraham at anu.edu.au
Sun Jun 15 11:48:40 CEST 2008


Please make more of an effort to follow conventions of written English - 
like spelling, punctuation and capitalization. You're asking for free 
help here, so you should make things easy for your reader. Following 
conventions does that.

> I want to simulate a peptide with nmr restraints in the bilayer containing chaps and a ganglioside, that resemble my nmr experimental results in bicelle!!!the partial charges if i want to redefine from the OPLS, i have total charge of molecule -1.577. How can i optomise the charge then?

Non-integral sums of partial charges mean the topology is broken. Fix 
that first.

> again, after minimisation in gromacs, the molecule has energy -2.16e-05, does the energy shows that the chaps is in a optimum geometrical condition?

It shows it's probably in a local minimum - but if your charges are as 
above then the energy surface on which it is a minimum barely has any 

> I am concentrating on the peptide and so i want to use UA model of OPLS for ganglioside and chaps, as we do in the lipid-BERGER force field. 
> thanks for suggestions, i am trying the way to use ffopls* files. More suggestions aboutthe opls parameterisation of chaps is requested,

The standard advice is here 
http://wiki.gromacs.org/index.php/Force_Fields and here 


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