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.
http://www.gromacs.org/Documentation/Errors?highlight=errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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