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NAMD vs GROMACS MARTINI parameters
- Marlon
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7 years 9 months ago #5754
by Marlon
NAMD vs GROMACS MARTINI parameters 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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- djurre
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7 years 9 months ago - 7 years 9 months ago #5765
by djurre
Replied by djurre on topic NAMD vs GROMACS MARTINI parameters
I'm not sure, since I am not very familiar with NAMD (and don't know how these files were created). But a bit of googling indicates that the "NBFIX" part of the "martini-all-nonb.par" files (which is where you found those values, I guess) has the following format:
type1 type2 Emin(Kcal/mol) Rmin(A)
So Gromacs and NAMD use a different formulation for the LJ potential: Gromacs uses c6/c12 input parameters. Even at constant "atom size" (= LJ sigma), both c6 and c12 can vary (check the Gromacs manual to see how c6/c12 and sigma/epsilono are related).
The fourth column in the NAMD files is comparible to the LJsigma and thus always constant. (Notice that it differs from sigma: sigma is the distance at which the potential crosses zero, the Rmin used in NAMD is where the potential is minimal (=force is zero). At least I assume.)
Notice you can also make Gromacs use sigma and epsilon as input. Change the [defaults] section on top of your itp to "1 2". Naturally you also have to convert all values.
type1 type2 Emin(Kcal/mol) Rmin(A)
So Gromacs and NAMD use a different formulation for the LJ potential: Gromacs uses c6/c12 input parameters. Even at constant "atom size" (= LJ sigma), both c6 and c12 can vary (check the Gromacs manual to see how c6/c12 and sigma/epsilono are related).
The fourth column in the NAMD files is comparible to the LJsigma and thus always constant. (Notice that it differs from sigma: sigma is the distance at which the potential crosses zero, the Rmin used in NAMD is where the potential is minimal (=force is zero). At least I assume.)
Notice you can also make Gromacs use sigma and epsilon as input. Change the [defaults] section on top of your itp to "1 2". Naturally you also have to convert all values.
Last edit: 7 years 9 months ago by djurre.
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