From: Jeffrey Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Wed Feb 16 2011 - 14:58:38 CST
Try running a short simulation with a timestep of 0.5-1.0 fs.
On 2/16/2011 1:15 PM, snoze pa wrote:
> Dear NAMD users,
>
> I am getting a constant error message in my membrane simulation. If
> I will imersed my protein into membrane then during melting of lipids
> there is no error message and simulation goes smoothly. However, If I
> will do the simulation with membrane only(melting of lipids) then it
> crashes everytime. So far I did 4 diffierent trials inculding the
> margin option in one of the simulation but it always gives me
> gfollowing error message.
>
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 20000
> FINISHED WRITING RESTART VELOCITIES
> ERROR: Constraint failure in RATTLE algorithm for atom 7948!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Exiting prematurely; see error messages above.
>
>
> Even after increasing the minimization steps to 10000, it gives me the
> similar error message for different time of the simulation.
>
> After carefully checking the atoM NAME, i found the atom is C22 from
> the lipids. So there is no error from TIP3 molecule.
>
> I will highly appreciate your help to resolve this problem. I already
> spend many cpu hours to get job done.
>
> Thanks in advance.
-- ====================================================================== Jeffrey J. Potoff jpotoff_at_chem1.eng.wayne.edu Associate Professor Wayne State University Department of Chemical Engineering and Materials Science 5050 Anthony Wayne Dr Phone:(313)577-9357 Detroit, MI 48202 Fax: (313)578-5815 http://potoff1.eng.wayne.edu ======================================================================
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