Well, you get a DV/DL result out in the normal mdout file if you set
ifsc=0, logdvdl=0
and the docs already list logdvdl under the softcore-related options, so
its reasonable-ish to have this apply only when ifsc!=0
In terms of having the needed functionality, and behaviour being consistent
with documentation, Dave's mdread2() fix is OK, however the need for this
is a symptom of the overall state of TI calculations between sander and
pmemd being fairly complicated and having something of a transitional
feeling about it.
I guess this is the way it is for backwards compatibility. Do we need to
keep supporting the old (multiple parmtop) way of doing it? Would a
rewrite simplify both code and docs? Plenty of big clusters are still on
AMBER12 or earlier, so bear in mind that changed made today may not reach
users until 2020 anyway.
New behaviour could be that ifsc = 0 is equivalent in output to
ifsc=1,scalpha=0, but with the actual softcore vdw calculation being
skipped in the code (invisibly to the user but of course saving a little
time).
Josh
On 17 December 2014 at 20:27, David A Case <case.biomaps.rutgers.edu> wrote:
> On Wed, Dec 10, 2014, Hannes Loeffler wrote:
> >
> > I have attached files for a sander14 run with TI/softcore. I get a
> > segfault when I try to run this. The problem is with logdvdl = 1. When
> > I delete this in the input files the jobs runs fine.
>
> The example has ifsc=0, so (at least in one sense) it is not
> really "TI/softcore". In any event, in the current code, combining
> ifsc=0 and logdvdl=1 won't work, because the arrays used by the logdvdl
> option
> are never allocated.
>
> Does anyone know the background here? Is logdvdl supposed to be used even
> when ifsc=0? If so, the log_dvdl() routine should probably not be in the
> softcore module, and (certainly) its allocations should not be
> sc_allocate().
>
> For now, I've put a check in mdread2() to disallow this combination.
> Moving the discussion over to the amber-developers list.
>
> ....dac
>
>
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Received on Thu Dec 18 2014 - 01:30:02 PST
