[gmx-users] EM in vacuum

Erik Lindahl lindahl at stanford.edu
Fri Feb 21 09:54:37 CET 2003


Gromacs actually adds the -FLEX_SPC option automatically for you when 
using cg (as far as I remember).

The reason why need it is that the normal water models like SPC and 
TIP3P are rigid, so even if the force was 1e+127 it wouldn't change the 
water geometry (but the integration would of course crash). To avoid 
this, we remove the rigidity during energy minimization and allow the 
bonds and angles to change. When you start the real dynamics run (from 
a minimized conformation) the molecule will be reset to its rigid state 

So, in short, unless you have water (molecules with SETTLE statements 
in general) you can forget about it.



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