GROMOS


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AcronymDefinition
GROMOSGROningen MOlecular Simulation package (computer simulation)
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It was done by analyzing frames from every 10 ps of simulation after the system reached stability and by subsequently selecting the central frame of the most populated cluster of system coordinates according to the RMSD values at cutoff 2 [Angstrom] of RMSD for cluster differentiation based on the GROMOS method.
Van Gunsteren, "A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6," Journal of Computational Chemistry, vol.
Choutko et al., "Definition and testing of the GROMOS force-field versions 54A7 and 54B7," European Biophysics Journal, vol.
GROMACS manual (http://www .gromacs.org/Support/Online_Manual) suggests that for allatom simulation of biomolecules water model TIP3P is suitable for AMBER and CHARMM, while TIP4P and SPC are more appropriate, respectively, for OPLS and GROMOS force fields.
Each force field is combined with four different water models SPC, SPC/E, TIP3P, and TIP4P, except GROMOS, which uses only SPC and SPC/E models.
In GROMOS one has different time scales for equilibration in SPC ([t.sub.eq] [approximately equal to] 7 ns) and SPC/E ([t.sub.eq] [approximately equal to] 10 ns), but in equilibrium the average values of RMSD are almost the same for both water models.
In GROMOS [E.sub.int], obtained by using SPC, is higher than SPC/E.
For AMBER (Table 3) SPc/E gives the lowest estimation for [DELTA][E.sub.elec], while the drastic water effect is observed in CHARMM (Table 5) and GROMOS (Table 6).
If they compensate each other as in the case of AMBER and GROMOS, then the absolute value of [DELTA][G.sub.bind] is small (Tables 3 and 6).
West Chicago Katarzynski (15 kills, 1 ace, 11 digs, 2 blocks); Gromos (7 kills, 4 blocks); Murphy (26 assists, 8 digs); M.Smith (6 kills, 2 blocks); J.Smith (17 digs, 2 aces)
West Chicago Katarzynski (11 kills, 1 ace, 9 digs); Murphy (25 assists, 1 ace); Gromos (6 kills, 3 blocks).