Re: Equilibration of the membrane bilayers with CUDA-support

From: James Starlight (jmsstarlight_at_gmail.com)
Date: Tue Sep 10 2013 - 09:06:11 CDT

The problem was solved by running minimization without CUDA (on cpu only).
So as I've told previously cuda-based namd has some problems with the
minimization implementation.

James

2013/9/9 James Starlight <jmsstarlight_at_gmail.com>

> Dear NAmd users!
>
> I've forced with the serious problem of the equilibration large systems
> mainly consists of the hydrated lipids.
>
>
> Briefly I've done long minimization after which tried to equilibrate my
> system in npt ensemble and obtained crash at the begining of the
> equilibration phase with the below listened errors
>
> colvars: Writing the state file "step6.1_equilibration.
> restart.colvars.state".
> colvars: Synchronizing (emptying the buffer of) trajectory file
> "step6.1_equilibration.colvars.traj".
> ERROR: Constraint failure in RATTLE algorithm for atom 14039!
>
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 8959!
>
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 66!
>
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 15321!
>
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 13670!
>
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 9380!
>
> Here you can find example of the bilayer which i"Ve tried to simulate in
> GPU-based regime
> http://www.charmm-gui.org/?doc=input/membrane_only&time=1378378701
>
> could someone tell me
>
> 1) What additions should I add to the conf files to increase stability of
> the simulations in case of gpu-based calculations ?
>
> 2) How I could performed simulation in the cpu-only regime (turned of the
> gpu) on the namd 2.7 compiled with the cuda support.
>
> Thanks for help
> James
>
>

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