On Mon, Mar 30, 2015 at 6:33 PM, Robert Wohlhueter <
bobwohlhueter.earthlink.net> wrote:
> Working my way through Advanced tutorial A5 (NEB) on a standalone,
> 4-processor, AMD-64 machine, running Amber14, under Ubuntu 14.04.
>
> In section 4, "heating up", I run into the following problem. Though
> everything appears to run alright under sander.MPI, in fact, inspection
> of the "-.out" files, any and all, shows that the temperature is
> remaining at 0 degK. I've checked and rechecked the syntax, especially
> the $wt namespace (&wt type='TEMP0', istep1=0,istep2=35000,value1=0.0,
> value2=300.0). Similar syntax, e.g. in the B0 tutorial ("02_Heat.in"}
> has worked fine..
>
> One additional disclosure, which might be at fault (if it is, then I
> really don't comprehend what's going on in NEB!) Because I have only 4
> processors (so, mpirun -np 4), I can't use "-ng 32", so I have broken up
> the tutorial's "groupfile" into 8 subgroup files, each comprising 4
> lines of the original groupfile. Is that kosher? Is there some reason
> this piecemeal approach might interfere with the replicate communication
> in a way that might prevent temperature ramping?
>
It shouldn't interfere in any way that I'm aware of, but note that this is
a very different simulation. In NEB, you have springs connecting *all* of
the replicates to make sure that none of them get too close to one another
along the reaction coordinate. By dividing into 8 subgroups, you are
eliminating the springs between where you cut up the total groupfile. So
it is definitely *not* the same thing that you are simulating.
If you take NEB *out* of your input file (so you are just running simple
dynamics), does the temperature ramp up as expected? It would also help to
see your exact input file to be of more help.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Mar 31 2015 - 05:30:05 PDT
