[gmx-users] Calculation Excess Chemical Potential of Bulk Water

[Justin Lemkul]

On 9/27/14 4:27 AM, Kim Q Hwan wrote:
> Dear all,
>
> 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 “forcefield.itp”
> #include “spce.itp”
> #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
> SO 1
>
> 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?

Replace [settles] with 3 constraints to achieve the same effect for the SO 
[moleculetype].

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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