[gmx-users] NPT equilibration with small cell

Miguel Caro miguel.caro at aalto.fi
Tue Feb 16 19:01:46 CET 2016


I was wondering if there is any reason why one should expect a constant 
pressure simulation not to work for a small cell. I am running a very 
small cell (1.2 nm^3) simulation because I need it as input for ab 
initio MD. I am trying to simulate NPT at 1 atm and it seems like my 
cell, a mixture of water and methanol, is expanding uncontrollably (to 
10 nm^3).

Is it not possible to do NPT for cells this small? I should add that NVT 
seems to work just fine for the same system.

These are the settings I am using for the pressure coupling:

Pcoupl = MTTK
tau_p = 0.2
compressibility = 4.5e-5
ref_p = 1.0

I have tried to do the same simulation with a supercell made up of 2x2x2 
periodic copies of my small cell and that seems to work fine. For that 
simulation, the only difference besides the cell size was the neighbors 
cutoffs, which I could increase from rlist = rcoulomb = 0.45, rvdw = 0.5 
for the small cell to rlist = rcoulomb = 0.8, rvdw = 1.1 for the 
supercell. For the small cell the cutoff radii are rather limited by the 
box size.

Thanks in advance,

*Dr. Miguel Caro*
/Postdoctoral researcher/
Department of Electrical Engineering and Automation,
and COMP Centre of Excellence in Computational Nanoscience
Aalto University, Finland
Personal email: *mcaroba at gmail.com*
Work: *miguel.caro at aalto.fi*
Website: http://mcaroba.dyndns.org

More information about the gromacs.org_gmx-users mailing list