[gmx-users] Implicit solvent - Gromacs 4.5.4
Mark.Abraham at anu.edu.au
Tue Feb 28 23:01:40 CET 2012
On 29/02/2012 1:11 AM, lina wrote:
> On Tue, Feb 28, 2012 at 10:07 PM, Steven Neumann<s.neumann08 at gmail.com> wrote:
>> Thank you Vedat!
>> Why do you use -DFLEXIBLE in md and in em?
>> Why dont you use constraint algorithm (LINCS) in your simulation?
> Otherwise, the system is easily explode with lots of LINCS warning.
That could well be the phenomenon referred to at the end of
http://www.gromacs.org/Documentation/Terminology/Blowing_Up. If you
equilibrate with a small time step, you should be able to simulate with
constraints, which is more efficient and probably a better model of real
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