[gmx-developers] innerloop code
cxing at ucdavis.edu
Thu Sep 7 03:37:27 CEST 2006
Hi Erik and David,
I really appreciate your emails and that helped me a lot! My work is getting
Thank you again
On 9/4/06, Erik Lindahl <lindahl at cbr.su.se> wrote:
> HI Chenyue,
> On Sep 3, 2006, at 1:39 AM, Chenyue Xing wrote:
> > Hi David,
> > Thank you for your quick reply.
> > I tried setenv and compared 2 simulations with exactly the same
> > initial structure and parameters (one w/ NOASSEMBLYLOOPS, one w/o it)
> > But the results seem to be different. Is this normal?
> To compare different loops or architectures, try running a single
> step and enable output of forces (use gmxcheck to compare them).
> There are multiple reasons for differences. First, the SSE code is
> performed entirely in 32 bit, modern compilers optimized for Pentium4
> and later mix 32 bit SSE and 64 bit SSE2 code, and old portable 387
> code is 80 bits internally, 64/32 bits externally.
> Depending on the order of operations generated by the compiler the
> rounding errors will be different, and since MD is intrinsically a
> chaotic process the trajectories will diverge exponentially with the
> number of steps. This is quite OK, since we are reproducing
> statistical properties and not trajectories of individual atoms.
> > Also, if I have assemblyloops enabled (not setting noassemblyloops
> > 1), can I actually find those assembly codes to read?
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