[gmx-users] with dispersion correction ...

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 30 00:48:20 CEST 2009

Jamie Seyed wrote:
> Dear all,
> I am simulation spc water system in NVE ensemble. During the grompp 
> stage, it gave me 2 Notes that rlist should be 0.1-0.3 nm bigger than 
> rcolumb and rvdw. So I chose rlist=0.9 and two others=0.7 also another 
> Note told me that I use vdwtye=shift and columbtype=PME-switch. That 
> solved the problem in this stage, however, in the mdrun step, I got a 
> Fatal error:
> -------------------------------------
> Program mdrun, Version 4.0.5
> Source code file: sim_util.c, line 842
> Fatal error:
> With dispersion correction rvdw-swith can not be zero for vdw-type=shift.
> -------------------------------------------------------------------------------------------------------
> Any idea about it and what value I should use for rvdw-swith ??

This is usually given in the literature: "Lennard-Jones interactions were 
shifted to zero smoothly between [rvdw-switch] and [rvdw]."  I don't know any 
force field for which a 0.7-nm vdW cutoff is really appropriate; most were 
parameterized with longer cutoffs.  I suggest looking into values designed for 
whatever force field you are using, and whether or not such a treatment of vdW 
terms is appropriate.


> Thank You in advance,
> Jamie
> ------------------------------------------------------------------------
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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