[gmx-users] some warnings

[Justin Lemkul]

On 10/25/12 8:52 AM, Albert wrote:
> hello:
>
>   I am using GBSA solvent for replica exchange simulation. However, I've got
> three wanrnigns when I generate .tpr file:
>
>
> NOTE 1 [file eq_11.mdp]:
>    Tumbling and or flying ice-cubes: We are not removing rotation around
>    center of mass in a non-periodic system. You should probably set
>    comm_mode = ANGULAR.
>
>
> NOTE 2 [file eq_11.mdp]:
>    Using GBSA with nstgbradii<1, setting nstgbradii=1
>
>
> NOTE 3 [file eq_11.mdp]:
>    Value of sa_surface_tension is < 0. Changing it to 2.05016 or 2.25936
>    kJ/nm^2/mol for Still and HCT/OBC respectively
>
>

Notes and warnings are different.  In this case, grompp is advising you that 
some of your settings are inappropriate.  For note 1, do what it says.  If you 
don't know why, Google "flying ice cube effect."  For notes 2 and 3, it is 
simply telling you that your settings are wrong and it is fixing them.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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