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David van der Spoel

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07/10/2018

10:27 AM GROMACS Bug #2568 (New): gmx editconf -rotate does not rotate the box
Using gmx editconf -rotate 0 90 0 -f conf.pdb -o out.pdb the box is not rotated.

06/13/2018

06:59 PM GROMACS Feature #2545: Should grompp fix periodicity of input files?
We could write a "check_for_inconsistent_shifts" function, in fact the code is there, use that in grompp to check inp...

06/12/2018

04:10 PM GROMACS Revision 1e629192: Let gmx nmeig print thermochemistry.
The quasiharmonic entropy analysis computes vibrational entropy.
Here we add translational and rotational terms in or...
07:31 AM GROMACS Bug #2533: GROMACS fails to build with lmfit-7.0
Sorry for the mess and not helping out a lot.
Might a fourth version be to go back to some intermediate solution t...

06/05/2018

11:41 PM GROMACS Bug #2542: Freezing does not work with constraints
This is indeed due to the com_groups = system option. You can circumvent this by using com_groups = water in your mdp...
11:25 PM GROMACS Feature #2545: Should grompp fix periodicity of input files?
OK, time to upgrade pbcutil/rmpbc to a c++ class?
Fixing the grompp (.tpr) and mdrun (.gro) output is relatively e...
08:44 PM GROMACS Feature #2545: Should grompp fix periodicity of input files?
Related to #2544
08:43 PM GROMACS Feature #2545 (New): Should grompp fix periodicity of input files?
If an input coordinate file is broken due to PBC, should grompp fix it? The issue is complicated if there are periodi...
02:11 PM GROMACS Bug #2544: gmx rmsf does not fix periodicity in reference structure
To reproduce:
gmx rmsf -f ub_traj.pdb -s broken.tpr -res -o rmsf_broken
gmx rmsf -f ub_traj.pdb -s whole.tpr -r...
01:56 PM GROMACS Bug #2544 (New): gmx rmsf does not fix periodicity in reference structure
If the periodicity in the input molecule that is use for fitting is not correct, the fit will be done on a broken mol...

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