Constraint failure in RATTLE algorithm for atom 268

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Oct 29 2010 - 05:46:16 CDT

It is customary to leave the mailing least in the recipients, so that others
may benefit from this conversation.

Some atoms are probably overlapping, which causes the bonds
to stretch (hence the error in the rattle algorithm).
If you turn the bonds of, then, due to the overlap, the system has a lot of
energy, hence the high velocity.
inspect which atoms give you the high velocity and try to move them by hand
(or see if they are too close to some other atoms).

Regards,
Ajasja

On Fri, Oct 29, 2010 at 12:00, surendra jain <sk_iitkgp_at_yahoo.co.in> wrote:

> Hi Ajasja,
>
> Thanks for your suggestion. I minimize the structure well with decreasing
> constraints on protein heavy atoms and then heat the system with a
> constraint of 20 kcal/mol on protein heavy atoms. turning the langevin
> pressure off does not give me the rattle error. does the rattle error has to
> do with npt ?
>
> I tried turning off the rigid bonds, but it gave me very high velocities
> for some atoms and the program terminated.
>
> Surendra
>
> --- On *Fri, 10/29/10, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>* wrote:
>
>
> From: Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>
> Subject: Re: vmd-l: namd-I : Constraint failure in RATTLE algorithm for
> atom 268
> To: "surendra jain" <sk_iitkgp_at_yahoo.co.in>
> Cc: vmd-l_at_ks.uiuc.edu
> Date: Friday, October 29, 2010, 12:11 PM
>
>
> This is more appropriate for the NAMD mailing list.
> But anyway, your system is not minimized, you probably have some steric
> clashes. Try to repeat the minimization, or perhaps try turning the rigid
> bonds off during the equilibration...
>
> Regards,
> Ajasja
>
> On Fri, Oct 29, 2010 at 06:39, surendra jain <sk_iitkgp_at_yahoo.co.in<http://mc/compose?to=sk_iitkgp@yahoo.co.in>
> > wrote:
>
> Hi everyone,
>
> I am trying to heat a protein+water system from 0K to 300K in NPT ensemble.
> but while starting the dynamics I get this error :
>
> Error : Constraint failure in RATTLE algorithm for atom 268
> ERROR: Constraint failure; simulation has become unstable
>
> and it gives this error for a number of atoms. I am using a timestep of 1
> fs for the heating step. Can anyone please tell me how to remedy this error.
>
>
> I am attaching the input file with the message.
>
> Thanks,
> Surendra
>
>
>
>

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