David van der Spoel
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- 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...
- 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...
- 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...
- 02:11 PM GROMACS Revision 69c5472c: Renamed entropy.* to thermochemistry.*
- This is a content-less patch to get the renaming history
correct in git.
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