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Michael Brunsteiner

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08/21/2018

11:07 AM GROMACS Bug #2619 (Closed): Segfault in gmx trjconv
Hi,
this is gmx 2018.2 on:
uname -a
Linux rcpetemp1 4.4.0-131-generic #157-Ubuntu SMP Thu Jul 12 15:51:36 UTC 20...

10/06/2014

10:56 AM GROMACS Bug #1611: gmx freevolume segfaults and dumps core

i downlaoded and install master (VERSION 5.1-dev-20141005-37573af) with git
and the issue appears to be resolved -...

10/02/2014

03:20 PM GROMACS Bug #1611: gmx freevolume segfaults and dumps core

> I have now reproduced the problem with the release version 5.0.2,
> but it works fine in master!
thanks! ... ...
02:54 PM GROMACS Bug #1611: gmx freevolume segfaults and dumps core

and the same issue on another desktop with debian testing, gmx 5.0.1 and c++ GNU 4.9.1 ...
gmx freevolume -f tes...
02:47 PM GROMACS Bug #1611: gmx freevolume segfaults and dumps core

the output i posted earlier was from our rocks cluser, see below for the specs ...
i should add that i get exactly...
01:49 PM GROMACS Bug #1611: gmx freevolume segfaults and dumps core

I should add that varying -radius from 0.05 to 0.1 or 0.0
does not change things ... some outcome:
Reading fram...
01:43 PM GROMACS Bug #1611: gmx freevolume segfaults and dumps core

i said its not predictible as in it happens for some systmes/trajectories
but not for others, doesn't mean its not...
10:57 AM GROMACS Bug #1611 (Closed): gmx freevolume segfaults and dumps core

trying to calc the free volume from trajectories of a system of a polymer blend
simulated at T=300K using gmx 5.0...

08/25/2014

04:14 PM GROMACS Bug #1583: gmx msd with mol flag requires excessive memory
> It certainly allocates O(nframes * nmols) memory.
fine, but what i don't understand is this ... if i don't use t...
02:25 PM GROMACS Bug #1583 (New): gmx msd with mol flag requires excessive memory

I find that calculation of diffusion coeffs using g_msd together with the mol flag
on my desktop (64bit ubuntu 12....

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