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

[Kim Q Hwan]

It works well.  Thanks

- Q-Hwan  

--  
Kim Q Hwan
Center of Nano-Liquid
Department of Physics & Astronomy
Seoul National University
Sent with Sparrow (http://www.sparrowmailapp.com/?sig)


On 2014년 9월 27일 Saturday at 오후 8:38, Justin Lemkul wrote:

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