Subject: Re: CCL:CCL

From: Wei Shi <weishi:at:umich.edu>
Date: Sun, 4 Jan 2004 01:20:41 -0500 (EST)

Hi, Rick,

Thanks for your help. Actually, my simulation is started from the PDB,
which includes crystalized water, ion, protein, and ADP. I add missing
residuals, and hydogen atoms. I assign potential type and partial charge
for one of the residuals which does not exist in the rtf file in the
CHARMm. Then, I do some steps of minization. In my system, I have not
added solvent water and not applied the PBC. The total number of atoms is
around 7000.

I heat my system in 5 ps from 240 K to 300 K, then perform equilibration
for 5 ps. After that, I perform 150 ps of NVE MD simulation production
run. The time step is 0.001 ps. The potential  energy is still drifting
down in the production run. For example, I calculate the average
potential in a time slot of 30 ps and the average is -17506 kcal/mol, the
value for the  next 30 ps is -17527 kcal/mol. This  energy drift, I
suppose, is not significant. The average difference is 0.1% in 30 ps.

By the way, I have tried NVT MD simulation. The potential energy  is still
drifting down even after 700 ps.

Generally, how long does it take to get equilibration from your experience
if you start the simulation from the X ray structure? I have read
many papers to hope to see the potential energy versus time without
sucess. Can you give me some reference papers?

Thanks very much for your help,

Wei Shi

On Sat, 3 Jan 2004, Rick Venable wrote:

> Certainly, a system with increasing T and decreasing potential energy is
> not at equilibrium, but obviously still relaxing.  Depending on the
> magnitude of the drift and the analysis, the results may be misleading.
>
> 	Some additional notes about CHARMM usage--
>
> NPT ensemble may be better, at least for equilibration after heating; a
> symmetric lattice such as cubic, truncated octahedron, or rhombic
> dodecahedron is usually appropriate for a solvated protein.
>
> I've observed quicker equilibration with velocity assignment (as opposed
> to velocity scaling).
>
> I guess it depends on your projects-- most of my CHARMM simulations
> start with coordinates from an extensive model building procedure
>
> On Sat, 3 Jan 2004, Wei Shi wrote:
> > I have one question for CHARMm about equilibration. Generally, the
> > calculation is started from the X ray structure, then heating,
> > equilibrating by velocity scale, and lastly production run without
> > velocity scale in the NVE MD simulation. However, I found that many of
> > the authors do not check the system to make sure it has been
> > equilibrated before they take the production run. Fro example, Some
> > authors observe the temperature is increasing with the potential
> > energy drifting down in the production run. However, they still do the
> > analysis. Is that a problem?
>
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