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two vdw potential
- tarraga
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1 year 4 months ago #9560
by tarraga
two vdw potential was created by tarraga
Hello users,
I want to implement two var der walls potential as described in a paper (dx.doi.org/10.1021/ct200593t):
"""The shift cutoff scheme (rshift = 0.9 nm and rcut = 1.2 nm) is applied to all LJ interactions, while the switch scheme (rswitch = 1.2 nm and rcut = 1.4 nm) is used for water-water BMH interactions.""" the last one implemented with a tabulated interaction function (table.xvg).
The system I want to simulate has peptides (P), SOL (water as BMW model) and Si (Silica bead surface).
My question is how to set these two vdw potentials in a mdp file.
Here is my mdp file with relevant lines but I duplicated "vdwtype" as "Shift" and "User" (table.xvg), which I do not know if it is correct.
I will appreciate any comment or suggestion on my problem.
Thankyou!
Tárraga Wilson
##############################
energygrps = SOL Si P
energygrp-table = SOL SOL
; NEIGHBOURLIST
nstlist = 10
rlist = 1.4
; NONBONDED-COULOM for SOL-SOL, SOL-P, SOL-Si, P-P and Si-P
coulombtype = PME
rcoulomb = 0.9
fourierspacing = 0.2
pme-order = 4
ewald-rtol = 1e-5
epsilon_r = 1.3
; NONBONDED-LJ for SOL-P, SOL-Si, P-P and Si-P
vdwtype = Shift
rvdw = 1.4
rvdw_shift = 0.9
; NONBONDED-BMW for SOL-SOL
vdwtype = User
rvdw = 1.4
#############################################
I want to implement two var der walls potential as described in a paper (dx.doi.org/10.1021/ct200593t):
"""The shift cutoff scheme (rshift = 0.9 nm and rcut = 1.2 nm) is applied to all LJ interactions, while the switch scheme (rswitch = 1.2 nm and rcut = 1.4 nm) is used for water-water BMH interactions.""" the last one implemented with a tabulated interaction function (table.xvg).
The system I want to simulate has peptides (P), SOL (water as BMW model) and Si (Silica bead surface).
My question is how to set these two vdw potentials in a mdp file.
Here is my mdp file with relevant lines but I duplicated "vdwtype" as "Shift" and "User" (table.xvg), which I do not know if it is correct.
I will appreciate any comment or suggestion on my problem.
Thankyou!
Tárraga Wilson
##############################
energygrps = SOL Si P
energygrp-table = SOL SOL
; NEIGHBOURLIST
nstlist = 10
rlist = 1.4
; NONBONDED-COULOM for SOL-SOL, SOL-P, SOL-Si, P-P and Si-P
coulombtype = PME
rcoulomb = 0.9
fourierspacing = 0.2
pme-order = 4
ewald-rtol = 1e-5
epsilon_r = 1.3
; NONBONDED-LJ for SOL-P, SOL-Si, P-P and Si-P
vdwtype = Shift
rvdw = 1.4
rvdw_shift = 0.9
; NONBONDED-BMW for SOL-SOL
vdwtype = User
rvdw = 1.4
#############################################
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