# Re: Namd list: Problem in equilibration stage

From: Aron Broom (broomsday_at_gmail.com)
Date: Thu Sep 27 2012 - 11:31:18 CDT

First, pressure will always be regulated at the expense of volume if
temperature is constant (well, assuming no particles can disappear), so it
doesn't make sense to consider pressure in NVT, outside of doing an initial
NTP equilibration to get the periodic dimensions right, and then swapping
back to NVT for performance reasons.

In terms of your density, a density of 1.00 g/ml might be what you would
expect for pure water at 298K and 1 atm (even then, TIP3P or whatever water
model you are using might not give this exact value). In your case,
however, you have a protein sitting in that water. So you need to think
about what you expect the density of the solution to be given the
concentration of your protein (which is probably unrealistically high since
one can only reasonably solvate with a certain sized box of water).
Consider that the density of protein is less than 1.00 g/ml and in general
the waters that are directly solvating the protein will also likely have a
lower density than bulk water since there will be increased order in that
region (mimicking the structure of ice to some extent).

So given all that, I doubt that 0.87 g/ml is really so unexpected (but you
can probably look at some reference values for proteins in solution and get
an idea of what the real value would be).

~Aron

On Thu, Sep 27, 2012 at 9:35 AM, Mariana Graterol <marianagraterol_at_gmail.com
> wrote:

> Dear NAMD users:
>
> I'm trying to balance my protein in a water box using periodic conditions;
> initially had a very low density (0.85 g / ml) and in the first run at 300
> K, many bubbles were formed.
> Then, I change the size of the box and prepared so that the density was
> 1.00 g/ml. Anyway, the first thing I did with my system was minimized and
> then perform the heating, if I heat the system in NPT ensemble, the volume
> increases initially, to leave me with a low density 0.87 g/ml. I've seen
> many posts on the list, articles, etc... that equilibration protocols using
> Langevin thermostat and barostat is reached at 300 K and 1 atm, in that
> first run, setting the volume to its proper value, not increasing it.
>
> It does not seem appropriate behavior, since, the equilibrium stage should
> be to set the initial system and bring it to reality, convergent values
> ​​in terms of temperature, pressure and density. But in my case, I do not
> see this.
> Furthermore, if I heat at constant volume (NVT), is greatly increased
> pressure (1000-1300 bar) and then the piston appears not to work and the
> pressure is regulated only at the expense of an increase in volume.
>
> Some might recommend a protocol for TP-volume set initially?
>
> I am using a restriction backbone atoms (not H) of my protein (K= 1500
> Kcal/mol.AA2) and some of the parameters show below:
>
> Thanks a lot,
>
>
>
> cutoff 12.000000
>
> switching on
>
> switchdist 10.000000
>
> pairlistdist 14.000000
>
> # Periodic boundary conditions
>
> cellBasisVector1 109 0.000000 0.000000
>
> cellBasisVector2 0.000000 111 0.000000
>
> cellBasisVector3 0.000000 0.000000 86
>
> cellOrigin 0.000001 0.000000 0.000000
>
> # Harmonic constraints
> constraints on
> consexp 2
> conskcol B (K= 1500 Kcal/mol. AA2)
> constraintScaling 1.000000
> conskfile C:\\Users\\pc\\Documents\\cal\\estructure.pdb
> consref C:\\Users\\pc\\Documents\\cal\\estructure.pdb
>
> # Langevin dynamics
>
> langevin on
>
> langevinTemp 300.000000
>
> langevinHydrogen off
>
> langevinDamping 5.000 (1/ps)
>
>
>
> # Constant pressure control
>
> langevinPiston on
>
> langevinPistonTarget 1.01325 (bar)
>
> langevinPistonPeriod 1000 (fs)
>
> langevinPistonDecay 500 (fs)
>
> langevinPistonTemp 300 (K)
>
>
> --
> * mari *
>

--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo


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