[gmx-users] Calculation Excess Chemical Potential of Bulk Water
Kim Q Hwan
kim.qhwan at gmail.com
Sat Sep 27 10:27:39 CEST 2014
I plan to calculate excess chemical potential of bulk water SPC/E model.
mu_water = mu_lj + mu_coulomb. mu_lj was successfully earned from test particle insertion method.
Problem arises in calculating mu_coulomb. I want to use g_bar method denoted in the Justin’s tutorial, changing vdW-lambda -> q-lambda.
I prepare 1000 water molecule(residue name SOL), and add 1 more water molecule(residue name SO) being used to calculate the mu_coulomb.
water.tpi.top topology file:
#include “so.itp” ; so.itp is same as the spce.itp <- cp spce.itp so.itp
[ system ] ; Name SOL and SO [ molecules ] ; Compound #mols SOL 1000
em_steep.mdp file(Free energy part):
; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda = 0 foreign_lambda = 0.05 sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 couple-moltype = SO ; name of moleculetype to decouple couple-lambda0 = vdw-q ; all interactions are turned on couple-lambda1 = vow ; turn off coulomb interaction couple-intramol = no nstdhdl = 10
grompp -f em_steep0.mdp -c water.tpi.gro -p water.tpi.top -o em_steep0 works well.
But mdrun -v -deffnm em_steep0 makes error and says that I use two SETTLE-provided Moleculetype.
I think that both molecule types SOL and SO use SETTLE algorithm and it makes error message.
So I want solution or advice. Is it impossible to use two molecule type with same SETTLE algorithm? If so, how I can calculate mu_coulomb of SPC/E water molecule?
Kim Q Hwan
Center of Nano-Liquid
Department of Physics & Astronomy
Seoul National University
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