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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========================================
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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