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

Lara Bunte lara.bunte at yahoo.de
Fri Sep 21 19:31:57 CEST 2012

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. 

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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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