From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Jun 04 2012 - 12:20:56 CDT
Now, with amber parm7 regular files, the system (protein in a water
box at 0.M NaCl concentration, and a few calcium++ ions), was
minimized with namd 2.9b.3 multicore, then heated gradually to 285K
with namd-cuda 2.9 (20,000 steps). Equilibration at such temp,, 1atm,
crashed with same error "namd-l: cuda_check_local_progress polled
1000000 times" at step 18400, out of planned 500,000. Setting of the
conf file was the same as for successful MD/amber parm 7 with
namd-cuda 2.8 in the past.
On Sat, Jun 2, 2012 at 9:06 PM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> With namd-cuda 2.9 on a shared-mem machine with two GTX-580 (Debian
> amd64) minimization (ts 0.1fs, wrap all) on a new system of a protein
> in a water box, crashed at step 2,296 out of planned 10,000. Changing
> to 2.9b3 multicore, the minimization worked well, ending at grad 1.5.
> I did not notice if this known issue at the time of beta tests had
> been fixed.
> francesco pietra
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