From: dimka (newyorkdimka_at_gmail.com)
Date: Sat Dec 24 2005 - 19:51:31 CST
Hi Shirley,
The atoms you're talking about may be "tangled". If that is the case, you
can use VMD's move atom/residue option to help bring the atom in the right
proximity.
When you plot the energies from NAMD log you'll see that this value
converges or reaches a plateau at some point. From experience, it takes
about 300-2000 steps to reach that point. Increasing the number of steps
won't do much.
-d
On 12/24/05, Shirley Li <li19104_at_yahoo.com> wrote:
>
> Dear NAMD experts,
>
> After finishing mimization, I tried running heating the system, but got
> the following message from heating:
>
> ERROR: Constraint failure in RATTLE algorithm for atom 29326!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Exiting prematurely
>
> I checked the minimized structure, the atom 29326 and the corresponding
> residue are too far from its two neighboring residues, just as what the
> related messages in NAMD archive suggested. The number of steps for the
> minimization was 26000 for fix-backbone MIN + 6000 for restraint-free MIN.
> I'm thinking of increasing them to 56000 + 26000 respectively. I have some
> questions here:
>
> 1) Is it possible to solve this problem by extending the minimization?
> 2) Are 56000 +26000 steps! too long?
> 3) Is there any other better way for this problem?
>
> Your help will be greatly appreciated.
>
> Shirley
>
> ------------------------------
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>
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