[gmx-users] Scaled 1-5 interactions
dommert at icp.uni-stuttgart.de
Sat Jun 6 14:06:56 CEST 2009
* David van der Spoel <spoel at xray.bmc.uu.se> [2009-06-06 08:06:26 +0200]:
> Florian Dommert wrote:
>> * Mark Abraham <Mark.Abraham at anu.edu.au> [2009-06-05 10:31:22 +1000]:
>>> Borys Szefczyk wrote:
>>>> Dear GROMACS Users,
>>>> I would like to use the OPLS force field, but with additional scaling
>>>> factor for the Coulomb 1-5 interactions for certain atoms. More
>>>> I want to use the standard 0.5 scaling for Coulomb and LJ 1-4
>>>> and 0.8 scaling factor for Coulomb 1-5 interactions. Is there a way to
>>>> do this within the topology file of Gromacs or do I need to modify
>>>> the code?
>>> I can't think of a way to do this natively. Trying to use fudge-LJ
>>> for 1-4 and pairs for 1-5 won't work (see 5.7.1 of manual).
>> Isn't the most naive way to define in the [ pairs ] section the further
>> requested 1-5 interactions ? However you will have to calculate the
>> epsilon and sigma of all the vdW-IAs, but this should not be a serious
> The VDW may work, but not differently scaled 1-4 and 1-5 coulomb
Where is the matter if I have a [ pairs ] directive in the itp file like this :
[ pairs ]
; ai aj fu
1 5 2 0.5 -0.11 0.13 0.30250 0.095865
1 6 2 0.5 -0.11 0.13 0.30250 0.095865
;this is are nonbonded intramolecular IAs separated by more than theree bonds
2 5 2 7.569 0.07200 0.02300 0.00000 0.00000
2 6 2 7.569 0.07200 0.02300 0.00000 0.00000
If I define nexcl=3 all the IAs in the second part of [ pairs ] are
already setup during the preprocessing as nonbonded IAs. Therefore I
have to define a correction term for the 1-5 IAs, if I want to have a
scaling of 0.8 and not "1.0". This can be achieved by a corresponding
adaption of the parameters F_QQ, qi, and qj for every pair within a
The example above represents a possibility to achieve a scaling of 0.5
for the 1-4 IAs and a specific scaling for all further nonbonded IA
within the molecule. In my case I just wanted to adapt the charges,
therefore the last two columns in the second part of the examples are
set to zero.
As mentioned in my last mail this setup allowed my to define a new FF
based on an old one. From the OPLS parameters the FFs differ just in the
partial charges and the aforementioned "correction term" for the 1-n IAs
furthermore provides a possibility to keep the intramolecular
interactions for the old and new set of partial charges constant. Both
FFs yield equal potential energy for a single molecule in vacuum. This
implies that the forces within the molecule remain constant, too.
If would scale my FQQ with a factor of 0.8 for all the 1-5 IAs I would
have achieved the requested circumstance.
What do you think about this ?
>> I had a molecule and gathered other charges. However as this new charge
>> distribution should not distrub the intramolecular energy landscape I
>> first defined all intramolecular nonbonded interactions within this
>> directive. This finally yielded exactly the same energy as the old force
>> field parameters.
>>> Setting the number of exclusions for a moleculetype to 4, in a
>>> forcefield with "generate_pairs = yes" and "fudgeLJ = 0.5" will
>>> probably see pdb2gmx get everything except the 1-5 interactions
>>> right. Then you post-process the .top from pdb2gmx in a (e.g.) perl
>>> script, using the [ bonds ] entries to recognize 1-5 interactions
>>> (which you add as [ pairs ]). You look up the normal LJ functions
>>> for those atom types, then invoking the combination rule and your
>>> 0.8 scaling and write parameters on the [ pairs ] entry for each 1-5
>>> pair. grompp will then blindly eat what you give it. Such 1-5
>>> interactions will be reported by mdrun in with the normal LJ
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> David van der Spoel, PhD, Professor of Biology
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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Institute for Computational Physics
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EMail: dommert at icp.uni-stuttgart.de
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