[gmx-users] (no subject)

[Erik Marklund]

Mark Abraham skrev:
> On 20/04/2010 4:39 PM, shahid nayeem wrote:
>> Dear All
>> I am learning molecular simulation using Gromacs. when I complete my
>> simulation, How can I check that my simulation run was o.k. and the
>> output so obtained can be trusted. Is there any easy calculation, which
>> could be performed.
>
> No. These tend to be "how long should a piece of string be?" 
> questions, unfortunately.
>
> The best thing to do is to have the simulation objective in mind 
> before you touch a computer. Now you can hopefully make decisions for 
> the right reasons, and can grapple sensibly with assessing whether 
> you've achieved that objective.
>
> Mark
True. There are certain things that are fairly general though. For 
instance, see if the conseved thrermodynamic quantities for your 
simulated ensemble are converged. If not, the simulation may still be 
ok, but may not be long eniough.

-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/