[gmx-users] GROMOS96 parameters in itp file obtained from PRODRG

[Mark Abraham]

On 03/02/10 15:55, sulatha M. S wrote:
> Dear gromas users,
> I am new to gromacs and trying to run polyacrylate MD simulation. I
> obtained an itp file using PRODRG (gromos 96 force-field parameters).
> When I compare with the same forcefield parameters in the gromacs/top
> directory, they are far too off. For eg.
>
> [ bonds ]
> ; ai aj fu c0, c1, ...
> 2 1 2 0.125 13400000.0 0.125 13400000.0 ; CAC OAD
> 2 3 2 0.125 13400000.0 0.125 13400000.0 ; CAC OAE
> 4 2 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAC
> 4 5 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAA
> 4 6 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAG
> 7 6 2 0.153 7150000.0 0.153 7150000.0 ; CAH CAG
> 7 8 2 0.153 7150000.0 0.153 7150000.0 ; CAH CAI
>
> As I understand, the function type should be 1 and c1 values should
> correspond to the force constant for bond stretching. But here it
> corresponds to the pair wise non bond parameters as listed in the
> gromacs/top force-field file. Similarly,

The bonded function type can have a whole range of values. See table in 
section 5.7.1 of the manual. That and the parameters, and the form of 
the target forcefield have to be considered as a whole in judging 
acceptability.

It's quite conceivable that the same numerical values are used in a 
bonded interaction (in [bonds] above) and forming the parameters in 
non-bonded interaction (in the [atomtypes] in the ffG96XXXbon.itp file) 
for in this case both pairs can represent quantities whose dimensions 
are length and energy respectively.

> [ pairs ]
> ; ai aj fu c0, c1, ...
> 1 5 1 ; OAD CAA
> 1 6 1 ; OAD CAG
> 2 7 1 ; CAC CAH
> 3 5 1 ; OAE CAA
> 3 6 1 ; OAE CAG
> 4 8 1 ; CAB CAI
> 4 11 1 ; CAB CAL
> 5 7 1 ; CAA CAH
>
> there are no pair terms listed here in the pairs section.

Some forcefields generate these solely from the [atomtype] data.

> [ angles ]
> ; ai aj ak fu c0, c1, ...
> 1 2 3 2 126.0 770.0 126.0 770.0 ; OAD CAC OAE
> 1 2 4 2 117.0 635.0 117.0 635.0 ; OAD CAC CAB
> 3 2 4 2 117.0 635.0 117.0 635.0 ; OAE CAC CAB
> 2 4 5 2 109.5 520.0 109.5 520.0 ; CAC CAB CAA
> 2 4 6 2 109.5 520.0 109.5 520.0 ; CAC CAB CAG
> 5 4 6 2 109.5 520.0 109.5 520.0 ; CAA CAB CAG
> 4 6 7 2 109.5 520.0 109.5 520.0 ; CAB CAG CAH
> For angles also the fu term is 2 instead of 1, although the angle and
> the force constant parameters are correct.
>
> Similar errors are there in the dihedrals section also.
>
> This means I need to almost fully edit the itp file I got from PRODRG to
> proceed further. Thank you in advance for any help and please clarify
> whether the itp file from PRODRG is unreliable even while using GROMOS96
> force field ?

There's no evidence of any error here. You should satisfy yourself from 
the contents of chapter 5 and the correct form of the GROMOS energy 
function that PRODRG is doing what you think it should. It looks to me 
like PRODRG is fine and you don't yet understand the form of what it 
should be producing. I suggest that you should do that learning.

Whether the numerical values will be sensible for MD simulations (as 
distinct from being expressed in a suitable form) is quite another question.

Mark