On 1/04/2012 5:51 PM, Acoot Brett wrote:
Hi Mark,
Then can you explain in which situation the calculation could be error
and how to avoid it?
One could write a book in partial answer to this question. There are
lots of things we don't yet know because we can't afford to run
calculations that might yield knowledge. Ultimately, a model of physics
is about as good as its capacity to reproduce findings from real
physics, and so the goal of simulators should be to use methods that
have been shown to do that well. Showing good performance can be tricky,
as converged equilibrium distributions are normally very expensive to
obtain. Also, different observables might require different methods for
good agreement with experiment, so there is no general answer for how to
do things right, unfortunately.
Mark
Cheers,
Acoot
*From:* Mark Abraham <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*Sent:* Sunday, 1 April 2012 5:47 PM
*Subject:* Re: [gmx-users] Possible error in the gromacs calculation
On 1/04/2012 5:44 PM, Acoot Brett wrote:
Dear All,
For the GROMACS 4.5.5, after installation the test link is
unavaliable, thus we cannot run the test.
For the AMBER, after we install it and run the test, although we can
pass most of the tests, we cannot pass all of the tests.
For GROMACS, can there anything wrong for the calculation, just as if
we cannot pass all the test for AMBER?
For the caluclation itself, in which situation we can get the wrong
calculation results? And how should we solve the problems if we the
calculation can give wrong results by default?
Unfortunately there is not an effective test set for GROMACS at the
moment. There is work taking place to get one, but it will not be
ready before 4.6.
Mark
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