From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Oct 18 2017 - 01:35:32 CDT
IMHO, if the results should be any meaningful, use explicit water.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Giacomo Fiorin
Gesendet: Mittwoch, 18. Oktober 2017 04:35
An: NAMD list <namd-l_at_ks.uiuc.edu>; Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
Betreff: Re: namd-l: building system with or without water for metadynamics
Dear Rabeta, you can also use metadynamics on examples that use ABF. Metadynamics has fewer restrictions and will work on the same variables that ABF does.
The tutorial you are referring to has a tiny system because it involves a 2D calculation, which takes a bit long for tutorial purposes. It is also a conversion of the basic PLUMED tutorial, so it has mostly the value of illustrating how to migrate between metadynamics implementations.
On Tue, Oct 17, 2017 at 8:06 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov <mailto:Joshua.Vermaas_at_nrel.gov> > wrote:
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
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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