[gmx-users] Re: DNA will not stay in the middle of the box (Nicolas)

[Berk Hess]

Hi,

Are you running in parallel with domain decomposition?
In that case it will probably not work, I forgot to add a check
for angular comm removal with domain decomposition.

It should work single cpu and with particle decomposition (mdrun -pd).

Berk

> From: p.woiczikowski at tu-bs.de
> To: gmx-users at gromacs.org
> Date: Thu, 11 Dec 2008 15:35:22 +0100
> Subject: [gmx-users] Re: DNA will not stay in the middle of the box (Nicolas)
> 
> Hi again,
> 
> I am aware that it is not quite physical to do so, but in this particular 
> project it really helps to use such a protocol.
> 
> Indeed, it worked perfectly in 3.3, so why should that not work with 4.0? May 
> there be a bug in 4.0?
> 
> Regards,
> Ben
> 
> >I think this question has been already addressed for proteins. Anyway, 
> >removing the COM motions of only one component of your system is very 
> >probably a bad idea. You should rather use position restraints. If you 
> >look in the mailing-list or the manual, you will quickly find how to do 
> >that.
> >
> >Regards,
> >Nicolas
> 
> 
> >> Hi,
> >>
> >> I simulate DNA molecules in water with counterions. To keep the DNA in the 
> >> middle of the box I had the following options in the input file:
> >>
> >> comm_mode = angular
> >> comm_grps=dna
> >>  
> > > For the old version (3.3.2) it worked but now (4.0.2) there are warnings 
> and 
> >> at the end the DNA doens't stay in the middle of the box.
> >>
> >> Can somebody help?
> >>
> >> Regards,
> >> Ben
> >>  
> -- 
> 
> 
> -------------------------------------------------------------------------
> Paul Benjamin Woiczikowski
> Department of Physical and Theoretical Chemistry
> Technische Universität Braunschweig
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> Germany
> 
> Phone:  
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