Re: Gradient Tolerance

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Oct 13 2004 - 14:43:04 CDT

Hi Matt,
Does namd give an error after the log entry you pasted below?

Just so I am on the same page, the psf and pdb file that have CO2 were
generated with psfgen with a segment for the protein, a segment for the
water, and a segment for the CO2?

>From the info you pasted in it looks like an extra line is in between the
C,O,O and the segment ID is not different from the water.

Also, just as a sanity check, the number of angles in the psfile
increase by one when the CO2 is added? and the bonds have increased
by two?

Just my thoughts
Brian

On Tue, 12 Oct 2004, mdcooper wrote:

> Hi there,
>
> I am to add one molecule of CO2 into my already minimized solvated system.
>
> When I do so, no matter where it is placed, trying to start up a minimization
> is impossible - I get:
>
> ETITLE: TS BOND ANGLE DIHED IMPRP ELECT
> VDW BOUNDARY MISC KINETIC TOTAL TEMP
> ENERGY: 0 2012.3514 1921.1975 1012.9252 21.8771 -64319.4483
> 6968.3134 0.0000 0.0000 0.0000 -52382.7838 0.0000
> INITIAL STEP: 1e-006
> GRADIENT TOLERANCE: -1.#IND
> BRACKET: 0 0 -1.#IND -1.#IND -1.#IND
> RESTARTING CONJUGATE GRADIENT ALGORITHM
>
> I have built the psf and pdb file myself and I have used psfgen on the new pdb
> file but both result in this problem.
>
> ATOM 14109 H1 TIP3 9188 89.987 63.838 25.302 1.00 0.00 SOLV
> ATOM 14110 H2 TIP3 9188 89.012 63.761 24.171 1.00 0.00 SOLV
> ATOM 14111 C1 CO2 9199 12.769 58.845 29.385 1.00 0.00 SOLV
>
> ATOM 14112 O1 CO2 9199 13.969 58.845 29.385 1.00 0.00 SOLV
>
> ATOM 14113 O2 CO2 9199 11.569 58.845 29.385 1.00 0.00 SOLV
>
>
> Has anyone encountered this before? As you can see the CO2 is well outside of
> the protein sphere and yet the problem remains.
>
> Thanks,
>
> Matt
>
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
*****************************************************************

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:18:24 CST