[gmx-users] linc warnings

Justin A. Lemkul jalemkul at vt.edu
Tue Dec 29 13:14:03 CET 2009

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.


> 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:



> Subarna
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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