[gmx-users] Water molecule can not be settled - mdrun error
jalemkul at vt.edu
Fri Sep 21 20:59:17 CEST 2012
On 9/21/12 1:31 PM, Lara Bunte wrote:
> Hi Justin
> I used this settings except of vdw-type = switch and rvdw_switch = 0.8 and with this settings grompp gives me two notes and one of this notes is inconsistent:
> NOTE 1 [file pr.mdp]:
> For energy conservation with switch/shift potentials, rlist should be 0.1
> to 0.3 nm larger than rvdw.
> Because I thought rlist hast to be 1.2 and rvdw hast to be 1.2 for my CHARMM27 force field.
Increase rlist as suggested to accommodate the algorithm. Since CHARMM does not
use charge groups (well, it uses single-atom charge groups) this isn't such a
big deal. For a force field like Gromos96, it matters a lot more.
> My second note is:
> NOTE 2 [file pr.mdp]:
> The sum of the two largest charge group radii (0.079505) is larger than
> rlist (1.200000) - rvdw (1.200000)
> which I sadly don't understand.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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