NAMD / GROMACS parameter differences
- Marlon
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Topic Author
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7 years 9 months ago #5753
by Marlon
NAMD / GROMACS parameter differences was created by Marlon
Hello,
I am currently trying to translate a NAMD system to GROMACS and am struggling with the parameters.
Indeed, I don't understand one thing concerning non-bonded parameters which seem, at first glance to me, problematic.
The crossterms, in martini_v2.2.itp are for example:
P5 P5 1 0.24145E-00 0.26027E-02 ; supra attractive
P5 Nda 1 0.21558E-00 0.23238E-02 ; attractive
The crossterms, in the parameters I found at www.ks.uiuc.edu/Training/Tutorials/martini/ for NAMD, are:
P5 P5 -1.33843000 5.27557163
P5 Nda -1.19503000 5.27557163
I'm okay with struggling a bit to get the units right, because there's obviously a conversion to do there. But that isn't what is troubling me.
Why is there, for the NAMD parameters, the same "5.27557163" twice while there's no duplicate parameter for the GROMACS ones ? This "5.27557163" is also there for the rest of the crossterms (all of them), shouldn't they vary at some point ?
After conversion, one of the parameters will also stay the same and that is something I do not observe in the original MARTINI for GROMACS parameters.
What did I miss ?
I am currently trying to translate a NAMD system to GROMACS and am struggling with the parameters.
Indeed, I don't understand one thing concerning non-bonded parameters which seem, at first glance to me, problematic.
The crossterms, in martini_v2.2.itp are for example:
P5 P5 1 0.24145E-00 0.26027E-02 ; supra attractive
P5 Nda 1 0.21558E-00 0.23238E-02 ; attractive
The crossterms, in the parameters I found at www.ks.uiuc.edu/Training/Tutorials/martini/ for NAMD, are:
P5 P5 -1.33843000 5.27557163
P5 Nda -1.19503000 5.27557163
I'm okay with struggling a bit to get the units right, because there's obviously a conversion to do there. But that isn't what is troubling me.
Why is there, for the NAMD parameters, the same "5.27557163" twice while there's no duplicate parameter for the GROMACS ones ? This "5.27557163" is also there for the rest of the crossterms (all of them), shouldn't they vary at some point ?
After conversion, one of the parameters will also stay the same and that is something I do not observe in the original MARTINI for GROMACS parameters.
What did I miss ?
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