[gmx-users] (no subject)

Atom News atomnews at hotmail.com
Sat Mar 9 19:46:18 CET 2002


thank you for your explaination. Unfortunately, I did not save the 
velocities it means I can not restart the simulation from the last frame? Do 
I have to start from beginning? If so, what should I do to avoid the crash 
again? (I used dt = 2ft)

Thank you in advance.


>From: Erik Lindahl <lindahl at stanford.edu>
>To: Atom News <atomnews at hotmail.com>
>CC: gmx-users at gromacs.org
>Subject: Re: [gmx-users] (no subject)
>Date: Sat, 09 Mar 2002 10:38:48 -0800
>Atom News wrote:
>>I have simulated the protein in water. After 362ps, I got the message:
>>Water molecule starting at atom 1094 can not be settled.
>>Check for bad contacts and/or reduce the timestep.
>>Can you help me? Thanks.
>This happens when an atom in a water molecule moves too fast (i.e. the
>water rotates too much in a timestep.), so the SETTLE algorithm that
>constrains the water bond lengths and angle breaks down. It CAN happen
>just by chance once in a blue moon in very large systems (in that case
>it will probably help if you restart from the last position in your
>trajectory, simply because you'll take a *slightly* different path in
>phase space the next time). Usually it's because your timestep is too
>large though (more than 2-3 ps), or because the water molecule is
>bumping into something.
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