Equilibration of the membrane bilayers with CUDA-support

From: James Starlight (jmsstarlight_at_gmail.com)
Date: Mon Sep 09 2013 - 10:16:40 CDT

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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