[gmx-users] Water molecule can not be settled - mdrun error

[Justin Lemkul]

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

-- 
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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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