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

[Justin A. Lemkul]

Mark Abraham wrote:
> 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.

And in addition, the most problematic section of a PRODRG topology is the 
[atoms] - the charges and charge groups are often unsatisfactory, requiring 
manual adjustment and validation (as you should, anyway, but the face-value 
parameters are often inconsistent with the original force field).

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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