Hi,
I am having a problem understanding the GROMACS implementation of cutoffs
and switching functions - at least Im getting results I cant make sense of.
I have been running dynamics of a protein-water system rhombic dodecahedron
periodic boundary system with the twin range cutoff scheme.
I have been attempting to minimize coordinate snapshots from this simulation
and to get to a reasonable maximum force was using the switching function
version
of cutoffs (in addition to flexible waters and no constraints).
What Im seeing is a large difference in the coulomb energies which I do not
understand where it is coming from.
To pin this down I am running the following test cases from a minimized system
and
computing the energy using two inputs.
First, twin range cutoffs (I got the rlist = 0.01 from some gmxtest runs)
rlist = 0.01
coulombtype = cut-off
rcoulomb = 1.2
vdwtype = cut-off
rvdw = 0.9
Second, switched cutoffs
coulombtype = switch
rcoulomb_switch = 1.199
rcoulomb = 1.201
vdwtype = switch
rvdw_switch = 0.899
rvdw = 0.901
Twin cutoffs log energy:
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
7.03530e+04 4.33556e+04 4.98766e+02 4.81356e+03 5.41441e+03
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR)
2.27345e+04 0.00000e+00 2.44898e+04 0.00000e+00 -3.16338e+05
Potential Kinetic En. Total Energy Temperature Pressure (bar)
-1.44678e+05 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
Switched cutoff log energy:
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
7.03530e+04 4.33556e+04 4.98766e+02 4.81356e+03 5.41441e+03
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR)
2.27345e+04 0.00000e+00 2.46563e+04 0.00000e+00 -1.06533e+06
Potential Kinetic En. Total Energy Temperature Pressure (bar)
-8.93502e+05 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
In the initial computation of the energies there is a large difference between
the Coulomb (LR) component - Ive tried using switching ranges from -/+ 0.15 nm
but nothing
seems to reduce the difference in the coulomb LR from a near order of magnitude
- yet the above switch functions should be close to the cutoff function so I
dont
expect such a large difference.
Thanks
David
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