On 13/06/12 16:59, Justin A. Lemkul wrote:
On 6/13/12 10:48 AM, ms wrote:
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...
Ah, sorry - with everything being named "GPU" it threw me off. I guess I
should have known based on the energy terms. When running on GPU, very
little information is printed (something I've complained about before) -
you only get Potential, Kinetic, Total, Temperature, and anything
related to constraints. I think it's due to limitations in OpenMM, not
Gromacs (something that should be improved in upcoming versions).
A few things to look at based on the .mdp file:
1. No constraints? Even with a 1-fs timestep, you probably need to be
constraining all least the h-bonds.
Ok. We usually don't constrain with 1-fs timestep, and since the gmx
website said that most restrains were unsupported, I didn't feel like
adding them. Will ask about this here.
2. nstlist set to 2 is not going to give wrong results, but it's
incredibly time-consuming to do neighbor searching that often. A value
of 5 or 10 is probably more appropriate.
I have to ask why we use this value as default, and thanks for the tip
-however this seems not relevant now :)
3. COM removal of multiple groups can lead to bad energy conservation.
OK, good to know.
4. What happens when you use the Andersen thermostat? That's not
implemented yet for CPU calculations (though it was recently pushed into
the 4.6 development branch). Your comment regarding GPU is fine, but I
would think grompp would complain.
I am unsure of what do you mean. On the gmx website it reads:
"Temperature control: Supported only with the sd/sd1, bd,
md/md-vv/md-vv-avek integrators. OpenMM implements only the Andersen
thermostat. All values for tcoupl are thus accepted and equivalent to
andersen. Multiple temperature coupling groups are not supported, only
tc-grps=System will work."
So it seems that *every* choice of mine means "andersen" in that
context. Am I wrong?
5. Why not use dispersion correction?
True, why not? :)
Will give it a shot.
thanks!
m.
--
Massimo Sandal, Ph.D.
http://devicerandom.org
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