[gmx-users] how to create a dummy atom in the oplsaa force field?
leafyoung81-group at yahoo.com
Fri Oct 28 08:45:07 CEST 2005
Here is an example of a simple topology of 4 atoms, fixing 1st with
respect to no.2, 3, 4 atoms using 3out. I used the parameters from
ffamber port from Stanford. OPLSAA FF could be a better FF for making
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.8333
#define c6c12 6.04920e-01 3.38904e-04
[ atomtypes ]
opls_O O 0.0 -0.198148148 D c6c12
opls_C C 0.0 0.0 D c6c12
opls_A A 21592.4925 0.0 A c6c12
opls_X T 300.0 1.0 A c6c12
opls_CL Cl- 35.45300 -1.000 A 4.40104e-01 4.18400e-01
opls_NA1 Na+ 22.98977 1.000 A 3.32840e-01 1.15897e-02
opls_K K+ 39.09830 1.000 A 4.73602e-01 1.37235e-03
opls_MG Mg2+ 24.30500 2.000 A 1.41225e-01 3.74342e+00
[ pairtypes ]
opls_X opls_X 2 c6c12
[ moleculetype ]
[ atoms ]
;nr type resnr residu atom cgnr charge mass
1 opls_O 1 SPD O1 0
2 opls_A 1 SPD A1 1
3 opls_A 1 SPD A5 2
4 opls_A 1 SPD A6 3
; Dummy from from from funct a b c
1 2 3 4 4 0.050803 1.190606 0.044177
I have a small program to calculate parameters for type 3out dummy
parameters based on atom coordinates. If you happened to use this type,
I could email you in private.
leafyoung81-group at yahoo.com wrote:
>Yes. It was a bit complicated to define dummy atoms
>when I did it.
>Here is my advices.
>1. Add user-defined atoms in the bottom of
>opls_O O 0.0 -0.198148148 D xxx
>opls_C C 0.0 0.0 D xxx
>opls_O and opls_C are defined name, variable according
>to your preference. Just remember to set mass to 0.0
>and atom type as D(for dummy)
>2. In the topology, use your defined type where you
>want to be.
>[ atoms ]
> 1 opls_O 1 SPD O1 0
> 11 opls_C 1 SPD O1 12
>Don't put any bonded interaction to dummies. Dummy
>atoms only have non-bonded interaction with others.
>3. In [ dummiesX ] section, set the parameters for the
>positioning of the dummies (refer to manual)
>4. There are other things needs to taken care,
>non-bonded interaction is the most important one (at
>least, for me). Do you want that dummy atom to have
>interaction with others, or with specific ones? This
>will be set according to nrexcl in [ moleculetype ]
>section and [ exclusions ] section in the topology.
>Check this with the output of gmxdump and quick MD
>tests. Until you have been sure everything is in
>control, you may start the simulation.
>--- nanyu101 at sina.com wrote:
>> I am trying to find a right way to simulate my
>>zinc enzyme. There are several methods found in the
>>references and mailing lists, such as cationic dummy
>> atom approach. But how to create a dummy atom in
>>the parameter files? The munaul is very compact, I
>>can\\\'t understand it clearly. Thanks a lot.
>>all your bests,
>>gmx-users mailing list
>>gmx-users at gromacs.org
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/Computational Biology Lab
School of Biological Sciences
Nanyang Technological University
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