[gmx-users] Freezing groups and energy conservation

Erik Marklund erik.marklund at chem.ox.ac.uk
Sun Nov 9 22:16:32 CET 2014

Dear Francesco,

Not sure, but the fact that PR yields energy drift suggests that you need to decrease the time step. Are you running in single or double precision? Are you removing COM movement?

Kind regards,
Erik Marklund

Erik Marklund, PhD
Postdoctoral Research Fellow, Fulford JRF

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road

On 9 Nov 2014, at 15:01, Francesco Mambretti <francesco.mambretti at studenti.unimi.it<mailto:francesco.mambretti at studenti.unimi.it>> wrote:

Dear all, I read a discussion about that but there are no news since then,
so I would like to know if there have been recent improvements.


The problem is: in Gromacs (also in my 5.0.2 version) freezing groups and
obtaining energy conservation (even with a run explicitly in NVE,
cutoff-scheme =verlet and verlet-buffer-tolerance = 10^(-8) ) seem to be
incompatible. Is that true?

I simply want to freeze an FCC-like core, made of 13 Argon atoms interacting
via LJ, in a liquid supercooled (liquid arrangement of the 256 atoms of my
system but velocities rescaled to a temperature typical of a solid
configuration) system. The idea is that this nucleus (that should therefore
mantain its shape) should guide the system to crystallize.

Apart from using position restrains, other alternatives to do that?
In fact also position restraints cause to me a negative energy drift, in
this case.


Francesco Mambretti, LCP, University of Milan

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