On Wed, 2014-05-14 at 02:02 +0300, MURAT OZTURK wrote:
> Thank you very much for clarification. The bug explains the inconsistency I
> was 'sensing' in the files. I have NATOMS 86347 and then 43150 lines, for
> example. I will be recompiling in the morning. How would I make sure the
> patch is upstream?
The patch is upstream. See
http://ambermd.org/bugfixesat.html (update.2
for AmberTools 14).
Amber/AmberTools has an automatic updater script that manages patches as
well. If you just recompile Amber, the configure script will look
online for available patches and ask you if you want to apply them if
any are found. Simply say "yes".
>
> I can hack C/C++ but I am hopeless with FORTRAN, thanks for the format
> information too.
>
> By the way, I am not at all interested in vacuum minimization, I just don't
> see why it shouldn't work. It should run, at least until it explodes or
> something, it is merely meant as a sanity check on my side.
It doesn't work because it is not coded in pmemd.cuda. It may seem
rather striking, but in reality there are no electrostatic methods that
closely resemble vacuum conditions that Amber uses. The EEL functional
form for PME electrostatics is _completely_ different (and imposes
periodicity), as is the GB approach. None of these methods can really
be implemented efficiently via "first calculate vacuum electrostatics,
then add on a non-vacuum correction term" (at least I think), so
including support for vacuum calculations would actually require an
extra bit of coding.
Given the numerous problems with simulating in vacuo, and the fact that
vacuum calculations are supported in sander, no effort was made to
implement it in pmemd.cuda, AFAIK.
> As for placing ions, I find it preferable to have some concentration of
> ions rather than the mere number of ions required to neutralize the system.
> Given that, random placement is fine, so addionsrand use is preferable.
> Thanks for that tip too.
I typically do that as well. In that case, you can specify the number
of ions you want to use. So for a 10- protein, for instance, I would do
something like:
addIonsRand system Na+ 40 Cl- 30
to add 40 sodiums and 30 chlorides. (Note that "addIonsRand" works by
replacing solvent, so you must always solvate first).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed May 14 2014 - 05:30:04 PDT
