[gmx-users] (no subject)

[Erik Lindahl]

>
Hi,


> And the user manual tell me that the OPLSAA force field calculate the
> 1-4 interaction by scalling,and the [ pairtypes ] section of
> ffoplsnb.itp file is empty.Does it means the [ pair ] section in
> topology of my molecule should be empty?

No; it means that we don't have to specify any special 1,4 parameters 
in the actual force field files, but you still have to specify which 
atoms are involved in 1,4 interactions. (This is autmatic if you write 
the molecule as an rtp entry!)


>
> In the early,someone have told me that for OPLS I don't need to speicfy
> pairs, and you need nrexcl to be two.
> But why in the ffoplsaa.rtp file,the nrexcl is to be 3?

Almost all normal force fields should use nrexcl 3. This means we 
exclude normal nonbonded interactions with the first, second and third 
neighbor. The third neighbor (1,4 interaction) is then added again, but 
in the [pairs] section, which means it uses the 1,4 parameters.

If you don't specify and pairs and use nrexcl 2 this means you don't 
scale down the 1,4 interactions at all.

>
> If I build block in the rtp file,It must will creat a topology file 
> that
> contain a [ pair ] section that is not empty this time.
> Needn't I try to modify the nrexcl to be 2 for making my topology file,
> or just let nrexcl to be 3 ? when the pdb2gmx generate the topology 
> file
> for me,needn't I try to modify the [ pair ] section to be empty?
>

The pdb2gmx program will do all this automatically for you once you 
have added an rtp entry.

> You also refer that the oplsaa is rather restrictive with improper
> dihedrals.But when I want to keep the pyrrole ring planar during the MD
> simulation, should they be use for our type of conformations?
>

Probably, but I haven't studied the pyrrole conformations a lot myself. 
Check the Jorgensen group papers (references can be found in the 
ffoplsaa.itp file in share/top/) for details.


Cheers,

Erik