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Simulation with Polarizable Water crashing
- sourav
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7 years 11 months ago #5583
by sourav
Simulation with Polarizable Water crashing was created by sourav
Hello
Note: CHARMM/NAMD specific question
I am currently trying to replace the non-polarizable water given in NAMD martini tutorial with polarizable one in my CG simulations.
Although the relaxation with higher damping happens well, the production run with lower damping keeps showing "atoms moving too fast" error. However, the same was not the case with single bead CG water before with similar simulation parameters except the dielectric constant (reduced from 15 to 2.5 as per literature).
The relevant additions to the martini parameter files w.r.t polarizable water (converted from GROMACS to CHARMM format personally) are given below:
!!
NONBONDED
D 0.00 -1.195 2.35 ! DO NOT USE
POL 0.00 -1.195 2.35 ! DO NOT USE
NBFIX
.
.
POL Qda -1.33843000 5.27557163
POL SQda -1.33843000 5.27557163
.
.
!Representative data only, list too huge.
ANGLES cos
! B1 B2 B3 k theta0
!Polarizable water
!WP, WM = D
!W = POL
!ANGLE WP W WM
!theta = 0, k = 4.2 kJ/mol 2.1 kJ/mol = 0.50191204 kcal_th/mol
D POL D 0.50191204 0 cos
BONDS
!Polarizable water
!WP, WM = D
!W = POL
!ro = 0.14 nm = 1.4 A, k=50000 kJ/mol/nm^2 -> 25000 kJ/mol/nm^2 = 59.751434 kcal_th/mol/A^2
POL D 59.751434 1.4
!No addition to Dihedral or Improper section and exclusions not included as NAMD calculates by itself.
!!
Please let me know if anyone can help with this issue or has done the conversion and performed a successful production run themselves.
Thanks and regards
Sourav
Sourav
Note: CHARMM/NAMD specific question
I am currently trying to replace the non-polarizable water given in NAMD martini tutorial with polarizable one in my CG simulations.
Although the relaxation with higher damping happens well, the production run with lower damping keeps showing "atoms moving too fast" error. However, the same was not the case with single bead CG water before with similar simulation parameters except the dielectric constant (reduced from 15 to 2.5 as per literature).
The relevant additions to the martini parameter files w.r.t polarizable water (converted from GROMACS to CHARMM format personally) are given below:
!!
NONBONDED
D 0.00 -1.195 2.35 ! DO NOT USE
POL 0.00 -1.195 2.35 ! DO NOT USE
NBFIX
.
.
POL Qda -1.33843000 5.27557163
POL SQda -1.33843000 5.27557163
.
.
!Representative data only, list too huge.
ANGLES cos
! B1 B2 B3 k theta0
!Polarizable water
!WP, WM = D
!W = POL
!ANGLE WP W WM
!theta = 0, k = 4.2 kJ/mol 2.1 kJ/mol = 0.50191204 kcal_th/mol
D POL D 0.50191204 0 cos
BONDS
!Polarizable water
!WP, WM = D
!W = POL
!ro = 0.14 nm = 1.4 A, k=50000 kJ/mol/nm^2 -> 25000 kJ/mol/nm^2 = 59.751434 kcal_th/mol/A^2
POL D 59.751434 1.4
!No addition to Dihedral or Improper section and exclusions not included as NAMD calculates by itself.
!!
Please let me know if anyone can help with this issue or has done the conversion and performed a successful production run themselves.
Thanks and regards
Sourav
Sourav
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