[gmx-users] .top file for a mixed solvent

[Justin Lemkul]

On 11/4/13 5:25 PM, Ehsan Sadeghi wrote:
> Hi gmx users,
>
> I want to simulate ionomer is mixed solution of water and ethanol using gromos force field.
> I tired to follow the steps suggested on gromacs website, which are:
>     1- Determine the number of co-solvent molecules necessary, given the box dimensions of your system.
>     2-  Generate a coordinate file of a single molecule of your co-solvent (i.e., urea.gro).
>     3-  Use the -ci -nmol options of genbox to add the required number of co-solvent molecules to the box.
>     4-  Fill the remainder of the box with water (or whatever your other solvent is) using genbox.
>     5-  Edit your topology to #include the appropriate .itp files, as well as make changes to the [ molecules ] directive to account for all the species in your system.
>
> Here are the commands that I used:
>
> pdb2gmx -f ionomer-4.pdb -o ionomer4.gro -p ionomer4.top -i ionomer4.itp (ionomer-4.pdb is the pdb file for 4 ionomer molecule)
>
> pdb2gmx -f eth.pdb -o eth.gro -p eth.top -i eth.itp (eth.pdb is the pdb file for single ethanol molecule)
>
> editconf -f ionomer4.gro -o box.gro -bt dodecahedron -d 0.5
>
> genbox -cp box.gro -ci eth.gro -nmol 1000 -o phase1.gro
>
> genbox -cp phase1.gro -cs spc216.gro  -o solvated.gro
>
>
> At the end, I have the solvated.gro file with 4 ionomer, 396 ethanol, and 423 water molecules. I don't know how to proceed step 5 and generated a combine .top file. What should I do with [ molecules ] directive?

List the number of ETH and SOL, respectively, in whatever order they appear in 
the coordinate file.  You need to have #included the relevant .itp files for 
ethanol and water in the ionomer .top beforehand.  The water .itp file was 
probably added by pdb2gmx.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
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

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