[gmx-users] Final Temp = 303 K ?

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> Hi
> I was running the MD simulation and you the Berendsen method.
> Here is my .mdp file.
> 
> ; Temperature coupling
> Tcoupl                   = Berendsen
> tc-grps                  = Protein  Non-Protein
> tau_t                    = 0.1      0.1
> ref_t                    = 300      300
> 
> 
> But the final Temp = 303 K
> No matter I extend the simulation time, the final Temp = 303 K and it
> can not reach the ref_t = 300 K
> 
> Does it make sense?
> 

If this is the entirety of your .mdp file, then all the other options are 
defaults, including coulombtype = cutoff, which, as was just discussed today, 
leads to heating of the system of the magnitude that you are seeing.

-Justin

> 
> The simulation system is protein + ligand + counter ions.
> ligand is the 33-atom molecule.
> force field ffG45a3.
> 
> 
> Thank you
> Lin
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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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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