GROMACS version: latest
GROMACS modification: Yes/No
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I am a beginner in gromacs and
I want to Solvate my protein in trifluroethanol ,but I don’t know how to start ,can anyone help me ?
I have gone through the manual but I am confused.
Thank you in advance
Looking forward to get a reply
To main options:
If you go the gmx solvate route, your command will look something like:
gmx solvate -cp conf.gro -cs trifluroethanol.gro -o solvated.gro
Where conf.gro is your protein within a box of fixed size and trifluroethanol.gro contains the geometry of your solvent.
The trick that I’ve found works pretty well here is that the trifluroethanol.gro should have a single trifluroethanol molecule (with the atoms in the same order as the topology file you have for it) centered within and with its box dimensions fixed such that the box has a volume that is roughly that of a single trifluroethanol.
Alternatively you can follow the examples for packmol at: http://m3g.iqm.unicamp.br/packmol/examples.shtml
A final, slightly more complicated example is to generate a box of trifluroethanol using packmol (or other software) and a box with just your protein. Then use topotools in VMD to merge the molecules and taking care to remove overlaps (there is an example located here: https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---various-tips-tricks#TOC-Combine-multiple-data-files-with-overlap-detection-and-removal , take a look at the second example).
Hope that helps.