Regarding your original post:
> http://archive.ambermd.org/201402/0006.html
> I have run molecular simulation for ionic liquids 4 times (each step
5ns).
> Now I want to calculate density and energy for whole of the simulation.
How
> to combine the result in the different output file?
I believe you can use MdoutAnalyzer.py to do this:
MdoutAnalyzer.py <mdout1> <mdout2> ...
See the AmberTools manual for more details.
> Also I don't know how to compute conductivity of the solution from the
> output and I can't find anythings in the tutorials.
I think this can be done using the velocity autocorrelation functions of
ions (I assume you are talking about electrical conductivity), but that's
not something I have a lot of experience with. The next version of cpptraj
will be able to calculate velocity autocorrelation functions.
> In addition I compile amber with mpi in a cluster and when I run the
tests
> ,there are some errors .
You need to provide way more information - we can't really help unless we
know exactly what the errors are. Do the tests not run? Do they crash? Do
you just seem to get some differences in the output?
On Wed, Feb 19, 2014 at 7:17 AM, Saeed Nasiri <s.t.nasiri.gmail.com> wrote:
> Also I simulate two sort of neutral molecules. I minimize the system but in
> the simulation part an error was appeared.
> I have two question?
> 1) what is ' ... RESTARTED DUE TO LINMIN FAILURE ...' ?
>
Did you check your output? In it there is explicitly a hyperlink to a web
page on which this topic is discussed:
> ***** SEE http://ambermd.org/Questions/linmin.html FOR MORE INFO
*****
> 2) what is 'Error: Bad topology file. Sum of ATOMS_PER_MOLECULE does not
> equal NATOM.' ?
>
This can occur when atom ordering within molecules becomes non-consecutive,
and has been discussed on the list before (see e.g.
http://archive.ambermd.org/201308/0340.html). The 'fixatomorder' command in
cpptraj or the 'setMolecules' command in parmed.py can be used to repair
the topology.
Hope this helps,
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Feb 19 2014 - 07:30:02 PST
