[gmx-users] LINC warning

凌未风 grx1985 at qq.com
Thu Nov 19 08:33:56 CET 2015

Hi All:

I have some strange problems with LINC warning in my simulations. 
mdrun gave a  lot of LINC warnings and the simulation explored after 5 ns simulations, below is one of these warnings:
time 7397.74 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.008123, max 0.064785 (between atoms 1756 and 1755)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1761   1759   30.7    0.1269   0.1267      0.1250
I am a little confused, because this happened after several ns simulations, so I would suppose this is not an energy minimization problem. I searched the mailing list and I found that someone proposed that this may because of the pressure coupling. 

below is the temperature and pressure coupling I am using:
; Berendsen temperature coupling is on in two groups
Tcoupl              =  V-rescale ; Berendsen  
tc-grps            =  Lipids     Solvent 
tau_t               =  0.1    0.1     
ref_t               =  330.0    330.0  

Pcoupl              =  Berendsen
Pcoupltype          =  semiisotropic   
tau_p               =  1.0 1.0 
compressibility     =  4.6e-5 4.6e-5
ref_p               =  1.0 1.0

I am using gromacs407 with reaction field for the long range electrostatic interactions for some reasons. I am wondering if anyone could gave me some suggestions of how to solve this problem. 
Any help will be highly appreciated. 


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