[gmx-users] multiple forcefields

Yiannis ioannis.nicolis at free.fr
Tue Jun 22 21:12:04 CEST 2004

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.

> 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
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