Re: building system with or without water for metadynamics

From: Vermaas, Joshua (
Date: Tue Oct 17 2017 - 19:06:12 CDT

Tutorials tend to be aimed at being run with modest hardware
requirements. This is why water was likely excluded, as it greatly
reduces the atom count and lets the user see the evolution within the
simulation without a supercomputer getting involved. Do whatever is most
appropriate for your system.


On 10/17/2017 03:57 PM, Rabeta Yeasmin wrote:
> Dear NAMD users,
> I am trying to run meta-dynamics to find binding sites between a
> protein and a ligand. I am wondering if I should include water in the
> system. In the NAMD metadynamics tutorial files, there was no water in
> the system. That's why I am confused if I should build the system with
> or without water.
> Thanks very much.
> Rabeta Yeasmin

This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:43 CST