Re: Help! unstable simulation - ARG go nuts...

From: Gadi Oron (
Date: Wed Dec 17 2003 - 04:36:47 CST

Hi again, and a big thank-you for those who look into my problem...

On Wed, 2003-12-17 at 06:10, Jim Phillips wrote:

> Hi,
> It looks like this is your problem:
> unknown patch type PT1
> ERROR: failed to apply patch

> I think you meant to type TP1. If you do, you get:
> applying patch TP1 to 1 residues
> unknown atom type ON3
> add atom failed in patch TP1
> ERROR: failed to apply patch
> If I substitute the prot_na topology file for prot_lipid there are other
> atom types missing, but if you include them both then psfgen is happy.
> Hopefully this will fix your minimization problems.

Thank you for the info, it is really useful. As pointed by Alex, I
should really take a more careful look at the psfgen output, and insist
that everything is going smoothly.

You are right that the patches I use cause some mayhem, but I believe
that this is not the cause for the crashes. The proof for that is the
fact that I cannot simulate a single chain from the structure I have
shown, not using any patches and passing psfgen with no errors, and
still get the same behavior!

To illustrate it, I have prepared a file located HERE. It reproduces the
same crash, while psfgen passes with only a warning on badly guessed
coordinates (should this considered an issue?).

To use this file, extract, use psfgen < stepC.psfgen, then run
./ equil.namd.

The MD will crash after 20 simulation steps. But take a look at the
Arginines during the minimization, they become strangely distorted with
atoms as close as 0.1 A (!!).

Any idea someone?

Best regards.

================= Gadi ORON, PhD -o- Proteologics ======================
=========== gadi/at/ =========== +972 8 9475666 ===========
A prediction is worth twenty explanations.
		-- K. Brecher

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