[gmx-users] multiple forcefields

Nuno R. L. Ferreira nunolf at ci.uc.pt
Tue Jun 22 20:44:27 CEST 2004

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 
Do not use ffgmx2 for MD, only if you want to do some energy minimization on a 

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. ;)


Nuno Ricardo Santos Loureiro da Silva Ferreira
Grupo de Química Biológica 
Departamento Química
Universidade de Coimbra
"Do not worry about your difficulties in maths.
 I can assure you that mine are still greater."

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