On 13/06/12 16:36, Justin A. Lemkul wrote:
Here, you're not preserving any of the previous state information.
You're picking up from 2 ns, but not passing a .cpt file to grompp - the
previous state is lost. Is that what you want? In conjunction with
"gen_vel = no" I suspect you could see some instabilities.
This is interesting -I have to ask the guys who devised the group's
standard procedure :)
mpirun -np 8 mdrun_d -v -deffn 1AKI_production_GPU -s
1AKI_production_GPU.tpr
-g 1AKI_production_GPU.log -c 1AKI_production_GPU.gro -o
1AKI_production_GPU.trr
-g 1AKI_production_GPU.log -e 1AKI_production_GPU.edr
As an aside, proper use of -deffnm (not -deffn) saves you all of this
typing :)
mpirun -np 8 mdrun_d -v -deffnm 1AKI_production_GPU
That's all you need.
FFFFUUUU that's why -deffn it didn't work! silly me. Thanks!
I am using Gromacs 4.5.5 compiled in double precision.
I am very rusty with Gromacs, since I last dealt molecular dynamics
more than 1
year ago :) , so probably I am missing something obvious. Any hint on
where
should I look for to solve the problem? (Also, advice on if the .mdp
is indeed
correct for CUDA simulations are welcome)
I see the same whenever I run on GPU, but my systems are always implicit
solvent. Do you get reasonable performance with an explicit solvent PME
system on GPU? I thought that was supposed to be really slow.
>
Do you observe similar effects on CPU? My tests have always indicated
that equivalent systems on CPU are far more stable (energetically and
structurally) than on GPU. I have never had any real luck on GPU. I get
great performance, and then crashes ;)
Sorry, perhaps I wasn't clear. This was on normal CPUs! I was trying to
get the system working on CPU and to see how it behaved before diving in
the GPU misty sea...
thanks,
Massimo
--
Massimo Sandal, Ph.D.
http://devicerandom.org
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