lindahl at csb.stanford.edu
Tue Dec 9 18:57:01 CET 2003
We will have a look at it. It would be great if you could send me a
copy of the mdp file in question off the list, though.
On Dec 9, 2003, at 8:03 AM, 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
> and there are 2 temperature groups each with its own coupling defined
> Any ideas? Thanks
>> -----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
>> 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 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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