Hi, On Tue, Nov 20, 2018 at 2:45 PM John Whittaker < johnwhitt...@zedat.fu-berlin.de> wrote:
> Hi Justin, thanks for the reply and the good idea. > > I checked a configuration of my system using both force fields and, for > the information of anyone who may have a similar problem in the future, > found using gmx energy: > > CHARMM36 from Tom Piggot on GROMACS website: > > Energy Average Err.Est. RMSD Tot-Drift > --------------------------------------------------------------------------- > Bond 8026.4 -- 0 0 > LJ-14 3825.57 -- 0 0 > Coulomb-14 -66212.1 -- 0 0 > LJ (SR) -6600.53 -- 0 0 > Coulomb (SR) -238906 -- 0 0 > Potential -223757 -- 0 0 > Kinetic En. 101836 -- 0 0 > Total Energy -121921 -- 0 0 > > CHARMM36 official implementation from MacKerell lab website: > > Energy Average Err.Est. RMSD Tot-Drift > --------------------------------------------------------------------------- > Bond 8026.4 -- 0 0 > LJ-14 3825.56 -- 0 0 > Coulomb-14 -66212.1 -- 0 0 > LJ (SR) -6600.04 -- 0 0 > Coulomb (SR) -238906 -- 0 0 > Potential -223757 -- 0 0 > Kinetic En. 101836 -- 0 0 > Total Energy -121921 -- 0 0 > > So, from the PE/KE/E-total values, the force fields are equivalent for my > system of DPPC and CHARMM-TIP3P. But curiously, I noticed the LJ values > Indeed > are slightly different for each (LJ-14, 3825.57/3825.56) and (LJ (SR), > -6600.53/-6600.04). Should I concern myself at all with this difference? > Both single-point reruns were processed and ran using 5.1.2. > No, that's down at the level where the order of floating point operations dominates other considerations. Out of curiosity, I also grompp'd and reran using 5.1.5. This time I > received the exact same LJ-14 and LJ (SR) values as in 5.1.2 (but still > those small differences between the force field) but the overall values of > the potential energy for both force fields was different than in 5.1.2 (by > 14 kJ/mol). > > Is there a simple explanation for why this might happen? > Maybe. Depends in what component the difference lies, and whether any of the release notes points to a reason - see http://manual.gromacs.org/documentation/#older-releases Mark Thanks again in advance for any help. > > John > > > > > > > On 11/19/18 11:32 AM, John Whittaker wrote: > >> Hi all, > >> > >> I am trying to reproduce the pure DPPC bilayer data found in J. Chem. > >> Theory Comput., 2016, 12 (1), pp 405–413 (10.1021/acs.jctc.5b00935) > >> using > >> the recommended protocol given in the paper. > >> > >> Recently, I realized I made a mistake and have been using the CHARMM36 > >> forcefield provided by Tom Piggot here > >> ( > http://www.gromacs.org/Downloads_of_outdated_releases/User_contributions/Force_fields > ) > >> rather than the official CHARMM36 implementation found on the MacKerell > >> lab's site (http://mackerell.umaryland.edu/charmm_ff.shtml). > >> > >> From what I understand from its description in the force field > >> documentation and the accompanying paper, the version provided by Tom > >> Piggot should not affect my results because the lipid parameters from > >> CHARMM36 are unchanged (while the protein parameters are) and my system > >> consists only of water and DPPC. > >> > >> Am I right to assume that my results should be (theoretically) > >> reflective > >> of those that I would obtain from using the using the full CHARMM36 > >> force > >> field? > > > > The lipids should all be the same. A single-point energy/force > > evaluation under both force fields would confirm this. > > > > -Justin > > > > -- > > ================================================== > > > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Office: 301 Fralin Hall > > Lab: 303 Engel Hall > > > > Virginia Tech Department of Biochemistry > > 340 West Campus Dr. > > Blacksburg, VA 24061 > > > > jalem...@vt.edu | (540) 231-3129 > > http://www.thelemkullab.com > > > > ================================================== > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send > > a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.