I know that the released AMBER 12 works fine on gordon as we were using this extensively prior to burning our allocation… If you do not need newer features, try this; if you still have problems, I can look at how we compiled…
On Oct 25, 2012, at 10:56 AM, InSuk Joung <i.joung.gmail.com>
wrote:
> Here are some more trials
>
> ntpr=1 does not print even a single energy output.
>
> ntr=0: same problem
> ntb=2, ntp=1: same problem
> ntb=1, ntp=0: same problem
> ntb=2, ntp=2, ntt=2, tautp=1.0: same problem
>
> Minimization (imin=1) works fine.
>
> On Thu, Oct 25, 2012 at 12:10 PM, David A Case <case.biomaps.rutgers.edu>wrote:
>
>> On Thu, Oct 25, 2012, InSuk Joung wrote:
>>
>>> I installed amber from the master branch on Gordon(UCSD) and I have a
>>> problem in running pmemd.MPI. Here is my mdout file.
>>
>> Please try a run with ntpr=1 (and nstlim some small value, say 100). That
>> might give more information about where the problem is (i.e. before or
>> after
>> the first energy evaluation).
>>
>> You should also try changing some of the parameters (again, on a short run;
>> for example set ntb=1 and ntp=0; and/or set ntr=0) to see if you can narrow
>> down the problem.
>>
>> ....dac
>>
>>
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>>
>
>
>
> --
> Best,
> InSuk Joung
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Received on Thu Oct 25 2012 - 10:30:05 PDT
