[gmx-users] Water clustering

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jul 10 21:20:43 CEST 2009

Hi Taka,

I'd say you need to add some more water :) But in addition to that,
you definitely should run with pressure coupling in stead of at
constant volume.



2009/7/10 H T <takayama at ceres.ocn.ne.jp>:
> Hi, I am trying to calculate micelle formation with SDS molecules for
> all-atom simulation.
> 49 SDS monomers (will increase it later) were settled in 15nm x 15nm x 15nm
> box.
> And I put water molecules from spc216.gro to the box.
> Considering water density is 1g/ml, around 112800 molecules are required but
> only 3400 water molecules was settled (around 3%) with genbox command at
> maximum. With this configuration, the SDS molecules assemble but also water
> cluster appeared. After 100ps MD, there is a room occupied with no atoms
> (vacuum, phase separation) and it is a bit funny. (1) Increasing the number
> of water to a realistic value or (2) tuning the parameter to avoid spc water
> aggregation might be good, but I don't know how to do that. Please give me
> a rope for it. Thanks,
> taka
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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