[gmx-users] Amber force fields giving LINCS errors

[Justin A. Lemkul]

TJ Mustard wrote:
> 
> First off I am using gromacs 4.5. I will also post all of my files and 
> errors if they help.
> 
>  
> 
> If I run a protein in GROMOS96 all my md runs complete succesfully. But 
> if I change to any of the AMBER force fields I get LINCS errors in my 
> positional restraint md run. I have tried using shake, 1 fs step sizes, 
> -heavyh, and many more. Does anyone know what is going on here?
> 

A complete (but not overly lengthy) post will save everyone a lot of time. 
Based on the information you've provided here, I see now way to diagnose the 
problem.  The most important information to post would be your .mdp file. 
Certain settings can influence stability.  A description of the hardware, 
compilers used, etc. can also be useful.

-Justin

>  
> 
> The reason I want to use AMBER is the fact that I want to run md on the 
> 30s rybosome and amber converts RNA much easier than GROMOS force fields.
> 
>  
> 
>  
> 
> Thank you in advance,
> 
>  
> 
> TJ Mustard Email: mustardt at onid.orst.edu
> Cell: 509-879-4173
> 
>  
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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