VMD-L Mailing List

From: Raman Preet Singh (ramanpreetsingh_at_hotmail.com)
Date: Thu Jul 30 2020 - 13:29:52 CDT

Dear All,

I have been using the Solvate plugin to generate water box for my systems. This is the first time that I am looking to perform simulations in non-standard solvents so need your help.

I looked through the mailing list and the webpage on the Solvate plugin but still have several questions.

  1. For creating a pdb and psf of the solvent box, I need to equilibrate the box of solvent (or solvent mixture). For how long (10 ns or more?) and using which ensemble (NPT?) should equilibration be performed?
  2. Can the box size of the solvent be different (smaller or larger) from the box size of the final system (protein + solvent)? If yes, then how much difference is acceptable assuming that the final box size will be 50x50x50 angstrom.
  3. When a protein is inserted in the equilibrated solvent box, the protein will displace the solvent resulting in an increase in pressure. Does this actually happen?
  4. Can the strategy used for solvent mixtures be used to simulate conditions where the process need to be studied in gas phase (protein in N2, O2, CO2, N2+O2, etc….)?
  5. Solvent box key selection: Here, an atom which appears only once in a solvent mixture needs to be added. In case of water/acetone mixture, it is oxygen. But how do I proceed if there is a single solvent (only acetone), or if there is no such atom which appears only once (water and acetic acid, for example) or no common atoms (O2+N2 gases)?

Thank you in advance for your help.

Regards,
Raman