GROMACS development

10/17/2017

10:09 PM GROMACS Bug #2274: Mega - Flops accounting

There are already eNRNB terms for eNR_POLARIZE and eNR_ANHARM_POL.
eNR_UREY_BRADLEY, eNR_CROSS_BOND_BOND, eNR_CROS...

09:52 PM GROMACS Bug #2274: Mega - Flops accounting

While we're at it, I found this mathematics with indices into an enum in mdlib/sim_util.cpp:
inc_nrnb(nrnb, enr_n...

09:40 PM GROMACS Bug #2274: Mega - Flops accounting

The relevant field in ifunc.cpp is 0 for F_POLARIZE and F_ANHARM_POL, this is used to index the nrnb struct. I can ma...

10/13/2017

06:30 PM GROMACS Feature #2272 (Accepted): pdb2gmx does not accept tips3p as a water model

Despite being supported by gromacs, pdb2gmx does not accept tips3p as a water model. This should be fixed since it is...

10/11/2017

07:09 AM GROMACS Bug #2268: v-site construction ignore water fails for charmm force filed

There could be the unlikely case of a CH3-OH2+ molecule, where #nbonds != #H, but we don't want to treat such unexpec...

10/10/2017

10:54 PM GROMACS Bug #2268: v-site construction ignore water fails for charmm force filed

Good work Flaviyan, maybe you can check what happens with those lipids?
Obviously you could have been "lucky" with y...

10:52 PM GROMACS Bug #2268: v-site construction ignore water fails for charmm force filed

Official pdb files have elements in the last column but we are not fussy about reading it. We try to deduct it from t...

10:01 PM GROMACS Bug #2268: v-site construction ignore water fails for charmm force filed

Interesting how those old comments come back and bite you.
Anyway I do not recall why I did this a while ago, but ...

10/06/2017

10:52 PM GROMACS Revision dc7edb5f: Couple of fixes to make tests compile

Change-Id: Ib65372976c06a2eabdd1eb60c8a7015be343a736

09/12/2017

04:21 PM GROMACS Bug #2071: Low accuracy default settings yield incorrect liquid densities

I intend to get back to this within the near future by putting a person to work on this.