[gmx-users] gmx3.20beta1

[David van der Spoel]

On Tue, 2003-12-09 at 17:03, Marco Ceruso wrote:
> 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
will fix it.

for now, set annealing to 
no no
(for as many groups as you have)
> 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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-- 
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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