Water bubbles in NVT equilibration dynamics

From: Mariana Graterol (marianagraterol_at_gmail.com)
Date: Fri Aug 24 2012 - 18:52:28 CDT


I want to equilibrate my protein in a water box, using PBC, ions, and
everything to set up my molecular dynamics.

I noticed water grouping during my equilibration dynamics NVT. (It looked
like many bubbles -spherical spaces without water molecules- in my box); I
guess that something it's wrong with pressure/volume since I didn't carry
on control pressure before i started the NVT run of production.

I had understood that a protocol it was minimize-heating-equilibrate
temperature (NVT)- and finally I will do a production run to evaluate
certain residues in my system as time evolves.

Is it recommended or is it necessary first equilibrate my system at
constant pressure and temp. NPT, before I run NVT equilibration?
and how NAMD controls density in a water box? because maybe it was a drift
in density?

Thank you in advance for any help...

Lic. Mariana Graterol

PhD student. Universidad Central de Venezuela

* mari *

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