[gmx-developers] g_bar crash. Bug or Feature?

Shirts, Michael (mrs5pt) mrs5pt at eservices.virginia.edu
Mon Mar 3 23:10:14 CET 2014

If its g_bar, Sander is the person to go to.  Synchronizing g_bar with broader analysis features is on the (ongoing) todo list, and I haven't had anything to do with g_bar, really.

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

From: Mark Abraham <mark.j.abraham at gmail.com<mailto:mark.j.abraham at gmail.com>>
Reply-To: "gmx-developers at gromacs.org<mailto:gmx-developers at gromacs.org>" <gmx-developers at gromacs.org<mailto:gmx-developers at gromacs.org>>
Date: Monday, March 3, 2014 at 4:42 PM
To: Discussion list for GROMACS development <gmx-developers at gromacs.org<mailto:gmx-developers at gromacs.org>>
Subject: Re: [gmx-developers] g_bar crash. Bug or Feature?

No idea, sorry. Sander and Michael are probably the only people who've ever known! :-)


On Mon, Mar 3, 2014 at 8:01 PM, David van der Spoel <spoel at xray.bmc.uu.se<mailto:spoel at xray.bmc.uu.se>> wrote:

I have a problem with g_bar in 4.6.5

Program g_bar, VERSION 4.6.5
Source code file: /afs/hpc2n.umu.se/lap/gromacs/4.6.5/src/gromacs-4.6.5/src/tools/gmx_bar.c<http://hpc2n.umu.se/lap/gromacs/4.6.5/src/gromacs-4.6.5/src/tools/gmx_bar.c>, line: 1204

Fatal error:
Could not find a set for foreign lambda = 0.000000
in the files for lambda = 0.000000

We have
@ s0 legend "dH/d\xl\f{} fep-lambda = 0.0000"
@ s1 legend "\xD\f{}H \xl\f{} to 0.0000"
@ s2 legend "\xD\f{}H \xl\f{} to 0.0250"

@ s0 legend "dH/d\xl\f{} fep-lambda = 0.0250"
@ s1 legend "\xD\f{}H \xl\f{} to 0.0000"
@ s2 legend "\xD\f{}H \xl\f{} to 0.0250"
@ s3 legend "\xD\f{}H \xl\f{} to 0.0500"

@ s0 legend "dH/d\xl\f{} fep-lambda = 0.0500"
@ s1 legend "\xD\f{}H \xl\f{} to 0.0250"
@ s2 legend "\xD\f{}H \xl\f{} to 0.0500"

And so on.

Any clue?

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205<tel:%2B46184714205>.
spoel at xray.bmc.uu.se<mailto:spoel at xray.bmc.uu.se>    http://folding.bmc.uu.se
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