[gmx-users] gmx3.20beta1

[Marco Ceruso]

Hi all-
just wanted to test gmx3.20beta1
I tried an .mdp file that works fine with gmx3,14 and 3.15beta1
but I got this error message running grompp on it:

Fatal error: not enough annealing values: 1 (for 2 groups)

now i am not doing any annealing just md with temp and pressure coupling
and there are 2 temperature groups each with its own coupling defined
Any ideas? Thanks
marco

> -----Original Message-----
> From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
> Behalf Of David
> Sent: Sunday, December 07, 2003 3:05 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] another attempt to clarify rlist, rvdw, ...
> 
> 
> On Sun, 2003-12-07 at 19:20, m b wrote:
> > dear gmx-users,
> > 
> 
> > 
> > If I understand that correctly this means that
> > if nstlist>1 the difference between 
> > max(rvdw,rcoulomb) and rlist should alsways be 
> > greater than zero (the manual suggests 0.25 nm)
> > otherwise one runs the risk of gmx occasionally
> > not considering interactions between some atoms 
> > that are separated by a distance of less than rlist.
> > The approprate value for this distance will depend 
> > on the parameter nstlist (and on the system 
> > geometry, temperature, etc).
> > I wonder if it wouldn't be a good idea for gmx
> > to check (at best continiously during a simulation)
> > whether the relation between the parameter nstlist 
> > and the difference between max(rvdw,rcoulomb) 
> > and rlist is reasonable? AFAIK this is not
> > implemented in gmx, in fact it doesn't even
> > give a warning if I set nstlist to a high
> > value and at the same time have
> > max(rvdw,rcoulomb)=rlist.
> 
> Much depends on how one treats coulomb interactions.
> If one use cut-off, then a *charge-group* based list is made at step 0
> and used for nstlist steps. Making rvdw,rcoulomb > rlist will trigger
> the same list as having rvdw,rcoulomb = rlist, but additionaly the
> forces due to charge groups being between rlist and rcoulomb/rvdw are
> computed during neighborsearching (NS), stored and added to the forces
> at every step, until new NS is done. With shifts and reaction field it
> is the same. With PME the Coulomb is almost correct, the only error
> remaining being that atoms drifting together between NS are not taken
> into account until NS is done again.
> 
> 
> 
> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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