Oh nevermind, I found the --reverse-patch flag in amber_update.
On Wed, May 14, 2014 at 3:42 PM, MURAT OZTURK <murozturk.ku.edu.tr> wrote:
> So I couldn't wait and applied the patch from the bugreport that you have
> linked. It did solve my current issues. Now I can see the update.2 is
> available but is it OK to install it on top of leap.patch or should I start
> fresh with unpatched code?
>
> Thanks for all the input.
>
> Regards,
>
> Murat
>
>
> On Wed, May 14, 2014 at 3:25 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> 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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>>
>
>
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Received on Wed May 14 2014 - 06:00:05 PDT
