GROMACS version: 5
GROMACS modification: Yes/No
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Hi, I am preparing TFE (trifluoroethanol)-water binary mixture systems for different xw or water mole fractions. For example, I will use ntfe (no of TFE molecules)=400 in a 5 nm cubic box and vary no of water molecules according to xw. Two possible way for preparing such a system:
method-1: generate gro file for a single TFE molecule: tfe.gro; then-> gmx insert-molecules -ci tfe.gro -nmol 400 -box 5 5 5 -o box.gro; Then add water either using gmx solvate or gmx insert-molecules
method-2: generate tfe.gro; then-> gmx editconf -c -d 1.0 -bt cubic -box 5 -f tfe.gro -o box_tfe.gro; followed by-> gmx insert-molecules -ci box_tfe.gro -nmol 400 -o 400_TFE.gro -box 5 5 5
method-3: gmx editconf -c -d 1.0 -bt cubic -box 5 -f tfe.gro -o box_tfe.gro; followed by-> gmx insert-molecules -f box_tfe.gro -ci box_tfe.gro -nmol 399 -o 400_TFE.gro; here nmol=399, as one molecule is already present in box_tfe.gro
I have compared the results from three methods; resultant coordinates using method-1 and 2 are almost same, except one or two decimal places for one/multiple atom(s); but method-3 gives different coordinates.
I am having confusion regarding which method to choose. I will appreciate any help.