How can I create a water box around our system with desired dimensions with desired number of solvent molecules around it (say a 50A x 50A x 50A cubic box containing 1000 water moleclues.) using namd and vmd ?
I came across the following command:
package require solvate
solvate abc.psf abc.pdb -t 5 -o abc_wb
But, what does the flag, -t 5 mean here ? What distance does 5 represent? And also, is there a way to set the number of solvent molecules? Can anyone help me out.
Thanks in advance.
The -t option creates the water box dimensions such that there is a layer of water 5 Angstroms in each direction from the atom with the largest coordinate in that direction.
Hello Krithika,
I dont think vmd gives you much flexibility with the solvate plugin. If you want the desired number of water molecules for your system, I suggest you a workaround that I found quite useful. Start with packing your system in PACKMOL and separate the resulting pdb into two individual pdbs, one containing your system and the other containing water molecules only. In your psfgen script, build both the segments one after the other. The Psfgen package then combines these two into a single topology at the end. If your system contains charges, make sure that you have additional water molecules in your starting structure as ion addition would preferably replace some water molecules from your system.
Just try one of the 100 tutorials on how to prepare a system in VMD for a MD simulation.
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