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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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