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Floris Buelens

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  • Last connection: 06/11/2014

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06/11/2014

11:19 AM GROMACS Bug #1521: outdated energy quantities used for replica exchange
From my quick test, replica exchange probabilities (step n vs. n+1) differ by:
more than 5%: 19.6% of attempts
mor...
11:11 AM GROMACS Bug #1521 (Closed): outdated energy quantities used for replica exchange
As discussed on the gmx-developers list:
[...] exchange probabilities are calculated at the very end of the MD ste...

05/10/2013

02:51 PM GROMACS Bug #1245: Bug in REMD with particle decomposition
...and bear in mind this was a hacked solution that made my specific problem go away, not tested any further than tha...
02:37 PM GROMACS Bug #1245: Bug in REMD with particle decomposition
some formatting got lost there - the 'for' line should read
for(i=0; i<state->ngtc; i++)
If you're working with 4....
11:08 AM GROMACS Bug #1245: Bug in REMD with particle decomposition
Hi,
I replied on the mailing list but perhaps you missed it. Your symptoms sound a lot like a bug I reported back in...

01/16/2013

04:29 PM GROMACS Bug #1121: slow MD with sd integrator and GPU / verlet
thanks for the reply - I'm not convinced that explains the numbers though. Ignoring the GPU for now, here are some mo...
07:59 AM GROMACS Bug #1121 (Closed): slow MD with sd integrator and GPU / verlet
I'm seeing MD simulation running a lot slower with the sd integrator than with md - ca. 10 vs. 30 ns/day for my 47000...

03/15/2011

04:09 PM GROMACS Bug #635: position restraints output with gmxdump -sys is wrong
commenting out this line:
/* Set the parameter index for idef->iparams_posre */
il->iatoms[i*2] =...

01/07/2011

02:30 PM GROMACS Bug #635 (Rejected): position restraints output with gmxdump -sys is wrong
gmxdump output for position restraints is incorrect when the option -sys is used. Tested with 4.0.5 and 4.5.3. Steps ...

06/11/2010

02:32 PM GROMACS Bug #433 (Closed): replica exchange+constant pressure broken with one cpu per replica
When running replica exchange at constant pressure, the exchange routine (exchange_state) exchanges box size informat...

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