[gmx-users] multiple forcefields

[Derrick Guang Yuh Lee]

dear yiannis

interestingly enough, i am working w/ a DPPC layer from dr. tieleman as
well. i am curious though, how did you get the OPLS system to work? did
you simply add in the atoms of the DPPC lipids into the rtp data base w/
its corresponding data from the atp file? again, thank you and nuno for
your quick responses.



 - derrick


 derrick Lee
 faculty of Science
 Memorial University of Newfoundland
 k24dgyl at mun.ca / derrickglee at hotmail.com

"a teacher is never a giver of truth - he is a guide, a pointer to the
truth that each student must find for himself. a good teacher is merely a
catalyst."
                                                              - bruce lee

On Tue, 22 Jun 2004, Yiannis wrote:

> Hello,
> just to add my experience, I tried recently to use lipid.itp from P.
> Tieleman's site to model a box of polyunsaturated fatty acids using
> ffgmx force field. While I could use his dppc bilayer topology and run
> the simulation I had stability problems with my system. Most probably
> these instabilities (leading to crash after 200 to 400 ps) were due to
> my topology around the unsaturated bonds. I finally decided to give a
> try to the opls force field and I managed to get a stable fatty acid
> box, reproducing very well the experimental density. Of course the
> simulation will be much longer but it was just a test system.
> Ioannis
>
> > On Tuesday 22 June 2004 06:27 pm, Derrick Guang Yuh Lee wrote:
> >> dear gmx-users
> >>
> >> right now i am working with a dppc bilayer from dr. tieleman's website
> >> which requires the ffgmx forcefields, but i have a peptide from my
> >> boss
> >> which contains all the hydrogens, which is from experimental data so
> >> she
> >> wants all those hydrogen's kept, which i can only get to work and
> >> keep the
> >> protons there if i use the ffmgx2 forcefields, and obviously there is
> >> overlap between the two forcefields. is it at all possible to combine
> >> the
> >> two sets of forcefields without compromising either structures and/or
> >> calculations that will be done?
> >
> > Hi Derrick
> >
> > In fact ffgmx is a united atom f.f., so not all atoms are explicitly
> > defined.
> > If you really want to work with those H's, use OPLS, which is an all
> > atom
> > forcefield.
> > Do not use ffgmx2 for MD, only if you want to do some energy
> > minimization on a
> > structure.
> >
> > I'm not the right person to say if an all atom forcefield is better
> > than a
> > united one, like gromos96 or gmx f.f.
> > But, the number of good scientific publications using the later one,
> > is an
> > indication that we can't really say that working with all atoms is the
> > best
> > choice.  Do not forget, that the computational time increases very
> > fast with
> > the number of atoms present in the system to be studied, and that
> > united f.f.
> > were parametrized in that way. No loss of information, I mean.
> >  And eventually, you can add up the H's later.  But, as I said, I'm
> > just an
> > user. ;)
> >
> >
> > Regards,
> > Nuno
> >
> > --
> > **********************************************
> > Nuno Ricardo Santos Loureiro da Silva Ferreira
> > Grupo de Química Biológica
> > Departamento Química
> > Universidade de Coimbra
> > Portugal
> > www.biolchem.qui.uc.pt
> > **********************************************
> > "Do not worry about your difficulties in maths.
> >  I can assure you that mine are still greater."
> >                                    emc2
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>