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Alan Dodd

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12/01/2008

07:12 PM GROMACS Bug #264 (Closed): g_order not producing order parameters
Created an attachment (id=328)
TAR of input files and script used.
All pre-3.3 files I have can be processed quite h...

01/18/2007

12:37 PM GROMACS Bug #126 (Closed): Problem with skipping large chunks of trajectory
When using the -b option with a variety of Gromacs programs - currently all
tested - g_density, g_traj, trjconv - to...

09/01/2006

04:25 PM GROMACS Bug #68: bilayer crashing in 3.3.1 but not 3.2.1 mdrun
With the typo fixed, the bilayers have not seperated for at least 750ps. The
extra stresses must have been causing ...

08/31/2006

02:03 PM GROMACS Bug #68: bilayer crashing in 3.3.1 but not 3.2.1 mdrun
Created an attachment (id=72)
.itp for DOPC
You're quite right, there is a typo in the 'pairs' section. Am testing ...

08/24/2006

12:44 PM GROMACS Bug #68: bilayer crashing in 3.3.1 but not 3.2.1 mdrun
Created an attachment (id=67)
tar of tpr and run outputs from 3.3 and 3.2.1
12:41 PM GROMACS Bug #68: bilayer crashing in 3.3.1 but not 3.2.1 mdrun
I've always used surface-tension. pme_order was definitely patched, one of the
first things I checked.
Am attaching...

08/21/2006

05:31 PM GROMACS Bug #68: bilayer crashing in 3.3.1 but not 3.2.1 mdrun
Yes. These values are comparable to other stable runs I have. In retrospect,
the forcefield I'm using (ffgmx modif...

04/10/2006

01:32 PM GROMACS Bug #68: bilayer crashing in 3.3.1 but not 3.2.1 mdrun
Created an attachment (id=34)
tar of ener files from 3.2.1 and 3.3
This example is using 3.3 (patched) rather than 3...
01:21 PM GROMACS Bug #68: bilayer crashing in 3.3.1 but not 3.2.1 mdrun
Created an attachment (id=33)
3.2.1 tpr file that only crashes with 3.3 onwards
01:18 PM GROMACS Bug #68 (Closed): bilayer crashing in 3.3.1 but not 3.2.1 mdrun
Versions of Gromacs after 3.2.1 crash due to an expanding box, due to
seperation of a lipid bilayer. Changing elect...

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