Re: Wrong energies in CUDA version

From: francesco oteri (
Date: Thu Jun 03 2010 - 15:10:00 CDT

I think it is. I m currently running a simulation with the namd2.7b2 gpu
version and
i ve experienced no problem

PS.Pressure control is supported, but only in the case of isotropic cell
fluctuation (

2010/6/3 Jeff Wereszczynski <>

> Hello NAMD List,
> I am trying to get a CUDA version of NAMD running. We have access to
> a GPU cluster with each node having 8 CPUs and either a Tesla C 1060
> GPU or a Tesla C 2050, with the cuda 3.0 libraries installed. I was
> able to compile a namd executable using the with-cuda flag which runs
> and detects the gpu, but the simulation quickly crashes with RATTLE
> errors. I tried to do a minimization and I observed that the energies
> at step 0 were all correct except for the pressure, gpressure,
> pressavg, and gpressvg columns. As I continue the minimization these
> terms fluctuate wildly and the potential energy of the system explodes
> as the vdw terms increases drastically (atoms begin to overlap with
> one another).
> I know pressure controls do not work in CUDA NAMD, but I am running
> NVT so I would think that NAMD would ignore these terms. I've tried
> this with both 2.7b2 and the CVS version and got the same results.
> Additionally, I tried this simulation (same input files) on a local
> GPU with the pre-compiled binary and it worked fine (the simulation
> progressed and the pressure values were normal). One major difference
> was on our local computer we had CUDA 2.3, whereas on this cluster
> only 3.0 is available, could this be the cause of the problem? Does
> anyone have any ideas of other things I could try to get this to work?
> Thanks,
> Jeff

Cordiali saluti, Dr.Oteri Francesco

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