From: L. Michel Espinoza-Fonseca (
Date: Tue Oct 20 2009 - 09:36:00 CDT

Hi Valeria,

Hello everyone,
> I'm interested in working with a protein and water, using the coarse
> grained model. Previously, I built a CG protein model, using the VMD CG
> Builder. Later, I ran a vacuum simulation with NAMD, and I didn't have any
> problems.
> Now, I'd like to build a protein embedded in water, using the CG model.
> First, I built full atom protein and I placed it in a full atom water box.
> Next, I tried to do the CG model using the same procedure I explained
> before, with VMD CG builder, and I got a PDB file output. Finally, I did the
> PSF of this system using PSFGEN and the PDB file.
> When I wanted to run a NAMD simulation using this system, the potential
> energy seems to be too high, and the minimizations suddenly stops. so it
> never ends.
How high is your energy? You should take a look at the energy terms in your
log file. My suspicion is that your model was incorrectly built and two or
more beads are too close to each another and thus yielding a very high
potential energy.

> The problem seems to be that the waters don't move. The total number of
> atoms of the system is 36.000.
36,000 atoms or beads?

 As I just said, your CG model might be too crude and the energy
minimization engine is just unable to converge. One thing that might help is
to minimize the all-atom system first before proceeding with the
construction of the CG model.


> Please help me to solve this problems
> Best regards,
> Valeria Marquez.

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