[gmx-users] Water molecule can not be settled - mdrun error
lara.bunte at yahoo.de
Fri Sep 21 19:31:57 CEST 2012
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.
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.
----- Ursprüngliche Message -----
Von: Justin Lemkul <jalemkul at vt.edu>
An: Discussion list for GROMACS users <gmx-users at gromacs.org>
Gesendet: 17:33 Freitag, 21.September 2012
Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error
On 9/21/12 11:26 AM, Lara Bunte wrote:
> Hi Justin
> Sorry but I don't understand what you mean with "Despite being given the correct settings for CHARMM27, you're still not using
> them." I use exactly the settings Peter gave me in my last question. What is in this settings wrong and where could I find the right settings?
I posted this link before:
The link that Peter posted has proper vdwtype and rvdw_switch settings (which say the same as the above link):
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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