[gmx-users] evaporating system

Xavier Periole X.Periole at rug.nl
Mon Oct 20 21:42:59 CEST 2008

Hi Anthony,

I don't understand how you manage to simulate in the NVT ensemble
without using pbc or any other way to define the limits of your
system? How do you then make a difference with NVE?

To avoid molecules to go far far far away you can define a dummy
atom at the center of your system and define distance restraint.
The water molecules would not be able to further than a given
distance. You might have to define a lot of distance restraints, though!


On Mon, 20 Oct 2008 14:51:29 -0400
  "Anthony Costa" <acosta at vdov.net> wrote:
> hi all,
> 1) i have an isolated NVT system of a few thousands atoms which
> evaporates at some reasonably constant rate via the temperature
> coupling. the system is a droplet and is in vacuum (no pbcs). problem
> is: at some point the evaporated molecules are very far separated in
> space from the bulk droplet and i end up with some severe intertia
> tensor errors:
> Inertia tensor (3x3):
>   Inertia tensor[    0]={ 4.60394e+08, -6.62964e+06, -3.39990e+07}
>   Inertia tensor[    1]={-6.62964e+06,  1.33291e+08,  7.34221e+06}
>   Inertia tensor[    2]={-3.39990e+07,  7.34221e+06,  2.22036e+07}
> etc.
> in other codes (i'm fairly new to gromacs), a simple "outflow" (used
> to doing a lot of CFD) boundary condition was possible whereby at some
> distance from the center of the box, molecules were simply removed
> from the system. does this exist in gromacs, or is there some other
> way i might get at this issue?
> 2) i would also like to perform this simulation in the NVE ensemble by
> initially generating velocities after the NVT simulation (i usually
> warm up the droplet first via NVT). however, generating velocities
> performs VERY poorly, and the simulation temperature usually blows up
> within a dozen or so picoseconds, which i don't understand. the basic
> structure of the simulation is identical to the well performing NVT
> simulation save adding the necessary LINCS iterations. any ideas?
> thanks very much,
> anthony
> --
> Anthony B. Costa
> Purdue University
> Department of Chemistry
> 560 Oval Drive, #365
> West Lafayette, IN 47907
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

XAvier Periole - PhD

- Molecular Dynamics Group -
NMR and Computation
University of Groningen
The Netherlands

More information about the gromacs.org_gmx-users mailing list