Help! unstable simulation.

From: Gadi Oron (
Date: Thu Dec 11 2003 - 01:51:14 CST

Dear NAMD users,

For the last several days I am attempting to run a simulation
of a Zinc-finger protein. I have followed all the steps in the
tutorials, but in all the combinations I have attempted the
system explodes few steps after the minimization ends.

The errors are various, but the common ones are failure in RATTLE
algorithm and "atoms too fast".

I have put a file containing all the data needed to reproduce the
situation here (

The steps that I have done are:

1. Extract from vmd the 4 chains of 1FBV.pdb into chainA.pdb,
chainB.pdb, chainC.pdb and ions.pdb.
2. Use psfgen to patch the needed residues and prepare the PSF:
        psfgen < step1.psfgen
3. Run the simulation (equil.conf is the namd config file).

The last step always breaks, no matter what parameters I use (with/wo
water, timestep, rigid bonds, minimizing with fixed backbone)...

Any comment will be greatly appreciated!
Thank you.

================= Gadi ORON, PhD -o- Proteologics ======================
=========== =========== +972 8 9475666 ===========
History repeats itself -- the first time as a tragi-comedy, the second
time as bedroom farce.

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