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Electrostatic Calculation in Martini
- mohammadsb
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8 years 7 months ago #4900
by mohammadsb
Electrostatic Calculation in Martini was created by mohammadsb
Hi,
Is anybody knows how electrostatic will be calculated in Martini? So far I found out that Martini use shifted function for electrostatic as mentioned in FAQ but is it only consider real term or it is also consider self, correction and reciprocate space too? I would appreciate if anyone could help me or refer a GROMAX file so I could take a look at it.
Is anybody knows how electrostatic will be calculated in Martini? So far I found out that Martini use shifted function for electrostatic as mentioned in FAQ but is it only consider real term or it is also consider self, correction and reciprocate space too? I would appreciate if anyone could help me or refer a GROMAX file so I could take a look at it.
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- mnmelo
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8 years 6 months ago #4996
by mnmelo
Replied by mnmelo on topic Electrostatic Calculation in Martini
Hi Mohammad,
The Martini electrostatic interaction has no correction and no consideration of reciprocal space. It is a simple Coulombic pairwise interaction, with implicit dielectric constant of 15, and shifted to zero at 1.2 nm.
See section 4.1.5 in the GROMACS manual for more details on the exact shifting procedure (there is a nice image there, but only for manuals of versions < 5.0).
As for a GROMACS file, the best is perhaps to run mdrun with the -debug hidden flag. This will cause it to output tables with the potential and force functions it is using (you'll be looking for the ctab.xvg file, which contains the Coulombic interaction functions). Note that in this case the potential and force aren't scaled by epsilon. Also, the force is shown as the derivative of the potential, and not as minus that value (which is the format that GROMACS takes when accepting table input).
The Martini electrostatic interaction has no correction and no consideration of reciprocal space. It is a simple Coulombic pairwise interaction, with implicit dielectric constant of 15, and shifted to zero at 1.2 nm.
See section 4.1.5 in the GROMACS manual for more details on the exact shifting procedure (there is a nice image there, but only for manuals of versions < 5.0).
As for a GROMACS file, the best is perhaps to run mdrun with the -debug hidden flag. This will cause it to output tables with the potential and force functions it is using (you'll be looking for the ctab.xvg file, which contains the Coulombic interaction functions). Note that in this case the potential and force aren't scaled by epsilon. Also, the force is shown as the derivative of the potential, and not as minus that value (which is the format that GROMACS takes when accepting table input).
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