[gmx-users] Fw: Re: 1-4 scaling problem?

[ANINDITA GAYEN]

Hi all!! I faced a problem with the dmpc bilayer decreasing, and reason was the topology file c6,c12 to sigma, epsilon conversion. I recalculated my sigma and epsilons with 9 decimal places now according to the suggestion by chris neale, and the area is now around 60A2. I am extremely thankful to Chris and others who helped me to move out from this problem.

                                                              anindita 
--- On Tue, 27/5/08, chris.neale at utoronto.ca <chris.neale at utoronto.ca> wrote:

> From: chris.neale at utoronto.ca <chris.neale at utoronto.ca>
> Subject: Re: 1-4 scaling problem?
> To: aninditagayen at yahoo.co.in
> Date: Tuesday, 27 May, 2008, 8:51 PM
> You are welcome. Please post this to the mailing list,
> perhaps with  
> some more description of how things went wrong, so that it
> will be of  
> use to others.
> 
> Chris.
> 
> Quoting ANINDITA GAYEN <aninditagayen at yahoo.co.in>:
> 
> >
> >
> > thank you....................very much. The topology
> files are now   
> > corrected, and the bilayer is looking smart with area
> per lipid   
> > 59.6A2 after 50 ps. Hope the area will not be
> disturbed and my   
> > headache will go for ever!!!!!
> >
> >
> > --- On Mon, 26/5/08, Chris Neale
> <chris.neale at utoronto.ca> wrote:
> >
> >> From: Chris Neale <chris.neale at utoronto.ca>
> >> Subject: 1-4 scaling problem?
> >> To: gmx-users at gromacs.org
> >> Date: Monday, 26 May, 2008, 10:21 PM
> >> Great. I don't know how your excel spreadsheet
> works,
> >> but I have been
> >> working from the following equation, which I am
> pretty sure
> >> that I
> >> posted to the list at some point as a comment in
> the
> >> example for how to
> >> make these changes:
> >> sigma=power(c12/c6,1/6) and
> epsilon=c6/(4*power(sigma,6))
> >>
> >> You could try this in bash:
> >> echo "0.009357 0.00003609" | awk
> '{print
> >> ($2/$1)^(1/6),$1/(4*((($2/$1)^(1/6))^6))}'
> >> or, if you had a file with c6 in col1 and and c12
> in col2,
> >> then you
> >> could replace echo "0.009357 0.00003609"
> by
> >> cat file.c6.c12 | awk ...
> >>
> >> Please let us know how it works out,
> >> Chris.
> >>
> >>
> >> ANINDITA GAYEN wrote:
> >> > thank you, I know that the epsilon values are
> >> different , but i am getting these values from
> origin and
> >> excel sheet. I am rechecking these ones. And, i
> will also
> >> try the ffgmx and lipid.itp , but i also have
> protein that
> >> i have to insert within the bilayer with my
> experimental
> >> nmr restraints and so i have to use OPLS-BERGER
> only.
> >> >
> >> > Thank you very much for the reply, I am
> trying to
> >> apply it.
> >> >
> >> > Ms. Anindita Gayen
> >> > C/O Dr. Chaitali Mukhopadhyay
> >> > Junior Research Fellow
> >> > Department of Chemistry
> >> > University of Calcutta
> >> > 92, A. P. C. Road
> >> > Kolkata-700 009
> >> > India
> >> >
> >> >
> >> >       Meet people who discuss and share your
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> >> >
> >
> >
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> >
> >

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