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

[sulatha M. S]

 Hi !
>


I am trying to reproduce results from reported polyacrylate simulations from
literature. I have the values for bonded and non-bonded interaction
parameters along with the the charges on atoms. I edited the charges and
charge groups in the itp file. I would like to know whether in the [bonds }
section, I can edit the itp file and give the force constants for  the bonds
instead of the non-bonded force constants (which the PRODRG provides).
Similar edting for the angles and dihedrals sections would make the itp file
suitable for running MD simulations. I ran MD simaultions with the existing
itp file (with just editing the charges) , but simulation results were not
comapring favorably with the reported values).

I also would like to know, in the top file,
#include ffg43a1.itp
#include paa.itp

the order should be as given above, or the reverse
#include paa.itp
#include ffg43a1.itp

I read from the manual that, if any parameters are eneterd twice, the values
which are read the second time will be taken.
In addition, I read FAQ for PRODRG, but was of no help in trying to
understand the details of the ff parameters in the itp file it generates.
>From where I can get the information on the details of itp file generated by
PRODRG.

Thanking you for any help,

Sulatha



> 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
>
> --
> ========================================
>
> 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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