[gmx-users] Implicit solvent - Gromacs 4.5.4

[Mark Abraham]

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 
physics.

Mark