[gmx-users] linc warnings

[Justin A. Lemkul]

subarna thakur wrote:
> Hi
> My protein has a Fe4S4 cluster. I have been able to minimize the 
> structure using Steepest descent. The log file shows following message:
> Steepest Descents converged to Fmax < 2000 in 372 steps
> Potential Energy  = -4.1580605e+06
> Maximum force     =  1.7402682e+03 on atom 820
> Norm of force     =  3.0794989e+01
> -----------------
> But during the position restraining step, following Linc warning is 
> coming before stopping all-together

If EM worked nicely, then something else you are doing is incorrect.

<snip>

> the atoms 5437,5438,5439 are the FE atoms of the Fe4S4 cluster. these 
> atoms are rotating hugely and showing large rms.
> Please suggest how to tackle the FE atoms during simulation run ? 
> Without the metal cluster, the same protein is working fine under 
> simulation and there is no such linc warinings?
> 

Without seeing your .mdp file and perhaps even snippets of your topology 
pertaining to the Fe4S4 cluster, there's nothing else to say except please read 
the standard advice:

http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings

-Justin

> Subarna
> 
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-- 
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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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