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Use of bond vs constraints for BENZENE
- sdutta
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11 months 2 weeks ago #9631
by sdutta
Use of bond vs constraints for BENZENE was created by sdutta
I am trying to get density of BENZENE correct using martini3 but using harmonic bonds in between the beads instead of constraints. My force field looks like
;;;;;; BENZENE
[ moleculetype ]
; molname nrexcl
BEN 1
[atoms]
; id type resnr residu atom cgnr charge
1 TC5 1 BEN B0 1 0 26
2 TC5 1 BEN B1 2 0 26
3 TC5 1 BEN B2 3 0 26
[bonds]
; i j funct length
1 2 1 0.291 189840.76
2 3 1 0.291 204016.80
1 3 1 0.291 187587.45
I have followed this steps-
1. putting 4000 beads inside a box
2. Energy minimization and short nvt
3. NPT with vrescale thermostat and Berendesen barrostat.
Unfortunately I am not getting the stable density around 900 kg/m^3.
where as If I constrained three bond lengths this problem doesn't arise. Please help
;;;;;; BENZENE
[ moleculetype ]
; molname nrexcl
BEN 1
[atoms]
; id type resnr residu atom cgnr charge
1 TC5 1 BEN B0 1 0 26
2 TC5 1 BEN B1 2 0 26
3 TC5 1 BEN B2 3 0 26
[bonds]
; i j funct length
1 2 1 0.291 189840.76
2 3 1 0.291 204016.80
1 3 1 0.291 187587.45
I have followed this steps-
1. putting 4000 beads inside a box
2. Energy minimization and short nvt
3. NPT with vrescale thermostat and Berendesen barrostat.
Unfortunately I am not getting the stable density around 900 kg/m^3.
where as If I constrained three bond lengths this problem doesn't arise. Please help
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