From: Valeria Marquez (
Date: Tue Oct 20 2009 - 08:52:10 CDT

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.

The problem seems to be that the waters don't move. The total number of
atoms of the system is 36.000.

Please help me to solve this problems

Best regards,

Valeria Marquez.

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