On Tue, Feb 26, 2013 at 8:56 PM, Christopher Neale < [email protected]> wrote:
> Dear users: > > I am experimenting with the "Stockholm" lipid parameters (Slipids). I > downloaded the recommended .mdp file from the developers of this force > field ( http://people.su.se/~jjm/Stockholm_Lipids/Downloads_files/md.mdp) and > was surprised to see the treatment of non-bonded interactions: > > coulombtype = pme > rcoulomb = 1.0 > rlist = 1.0 > rlistlong = 1.6 > rvdw = 1.5 > rvdw-switch = 1.4 > vdw-type = switch > > it struck me as strange to have rlist < rvdw (I didn't even know that this > was allowed, but I tried it and it is) > Yup, that's what twin-range does. (Note that this is from their website, but their original paper would have > used rcoulomb = 1.4 and rlist = 1.4). > > When I run grompp version 4.5.5 with these parameters, I get the following > note: > > NOTE 2 [file empty.mdp]: > The sum of the two largest charge group radii (0.000000) is larger than > rlist (1.000000) - rvdw (1.500000) > > This system has only one Na and one Cl ion (chosen for simplicity during > mdp testing). By moving these ions apart and doing a 0-step mdrun, I was > able to verify that the LJ interaction energy moves from the LJ(SR) to the > LJ(LR) component for d>=1 nm and that this energy is non-zero until d>=1.5 > nm. > > I am asking if anybody sees a problem because (a) grompp threw a note, and > (b) even if this works alright for standard simulations, I just want to be > sure that if I get into more exotic parts of the gromacs code then I am not > likely to encounter situations in which this cutoff scheme introduces > problems (silent or otherwise). > It seems there's some issue with how that note is being triggered that bears investigation, in case there's further problems to uncover. Can you attach a tarball of grompp inputs to http://redmine.gromacs.org/issues/1164, please? (It may or may not be the same issue as that one, but they may as well be investigated together!) Mark -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
