Re: Help! unstable simulation.

From: Alexandre Vakhrouchev (
Date: Fri Dec 12 2003 - 03:16:55 CST


First of all look at the output of your psfgen script (it is attached as 'pfs.log').
You have some errors while loading coors from *.pdb files and when
you apply patch (I'm not familar with these error, perhaps other persons
can explain them more extensively).

So, in my point of view, these errors couse than not all coors in protein.pdb file
are set properly, and some atoms are to close too eache other. When minimization
is finished, those atoms are pushed away too fast, that's why namd session crahes.

I'm also intrested in solving this problem, because when i provided coors only for
a number of atoms in residue, and other coors were guessed, my simulation crashed
(guessed atoms were too close). Minimization didn't help in this case.
I solved this error by providing coors for all atoms,
depending on Rmin/2 values (from Van-der-Waals force field parametres), but i had to
write additional programm.

Are there more elegant solutions? Depending on what principles psfgen provides guessed



----- Original Message -----
  From: Gadi Oron
  Sent: Thursday, December 11, 2003 11:51 AM
  Subject: namd-l: Help! unstable simulation.

  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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