[gmx-users] Possible error in the gromacs calculation

Mark Abraham Mark.Abraham at anu.edu.au
Sun Apr 1 10:47:04 CEST 2012

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.


> Cheers,
> Acoot
> *From:* Mark Abraham <Mark.Abraham at anu.edu.au>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *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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