[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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