AW: Water bubbles in NVT equilibration dynamics

From: Norman Geist (
Date: Tue Aug 28 2012 - 01:26:25 CDT



Regarding the advices before, you should of course do a constant pressure
run some when in your simulation protocol. We usually do it like
mini->heat1->pressure->heat2->free cause the pressure can change the
temperature. I wouldn't follow the advice to let only the water move during
constant pressure. How should that work if there's a protein and ions inside
the solvent? Also, fixed atoms during constant pressure usually comes with
FATAL errors because of the coordinate rescaling and the resulting high
forces of colliding atoms. The "patch has become too small for original
patch grid" error will occur if your boxes initial density was extremely far
from ideal. Then, the box get smaller than the initial department for
parallelization. You can just restart the simulation from the latest restart
files then, as the departing is done again at simulation start, or to
prevent it from crashing already, you can use the margin parameter, but this
slows down the simulation. You have to test out.


Good luck


Norman Geist.


Von: [] Im Auftrag
von Jeffrey Potoff
Gesendet: Montag, 27. August 2012 17:01
Betreff: Re: namd-l: Water bubbles in NVT equilibration dynamics


One gets "bubbles" in these cases because they don't have enough water in
the system to give them a correct density of approximate;y 1 g/cm^3.
Running NPT may help, but it depends on how wrong one's original estimate
was for the number of required water molecules. If one is too far off,
they will have to deal with the infamous "patch grid error".

On 8/27/2012 10:23 AM, Ana Celia Vila Verde wrote:

Dear Mariana,

After minimization, one should always run an NPT equilibration where only
the water atoms are allowed to move. Only when the average volume of this
simulation is approximately constant can you proceed with a further NVT
equilibration, and then any runs you want. Note that the starting
configuration for the NVT equilibration should be obtained from the NPT
run by: 1- calculating the average volume of the NPT run once it has stopped
drifting; 2- finding a saved dcd frame where the instantaneous volume is
very close to the average one.

I hope this helps.


On 8/25/12 1:52 AM, Mariana Graterol wrote:



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 *
Jeffrey J. Potoff          
Associate Professor  and Director of Early Engineering Programs
Department of Chemical Engineering and Materials Science
Wayne State University                       5050 Anthony Wayne Dr
Detroit, MI 48202                     TEL: (313) 577-9357

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