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

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 3 15:09:58 CET 2010



sulatha M. S wrote:
> 
> 
>     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 guess I don't fully understand your problem.  There are no nonbonded force 
constants in the [bonds] section.  The bonds you have shown (a carbonyl and some 
C-C group, presumably) corresponds exactly to the bonded parameters given in 
ffG43a1bon.itp:

#define gb_5        0.1250  1.3400e+07
; C  - OM       1000

#define gb_26       0.1530  7.1500e+06
; C, CHn  -   C, CHn    800

 From everything I can see, the PRODRG bonded parameters are produced as they 
should be.

> 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
>  

Neither.  The proper order is the first one you've shown, but the capitalization 
and syntax are incorrect.  What you want is:

#include "ffG43a1.itp"
#include "paa.itp"

The manual, Chapter 5, is your friend here.

> 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.
>  

There is a paper for PRODRG.  Surely it is cited somewhere on the PRODRG server. 
  But as far as the bonded parameters are concerned, it appears that PRODRG is 
reading from a library of bond types.  Perhaps if there are some unknown bonds 
it will generate some generic parameters, but otherwise I don't see anything 
wrong or unexpected with what you've got.

-Justin

> 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 <http://vt.edu/> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/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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