[gmx-users] What can I to do with the problem: lincs warning and water can not be settled?

2009-06-19 Thread xiao shijun 
hi,
  The simulation was OK. But when I changed the epsilon of some atoms to get
rid of LJ, lincs warning emerged as:
step 116 ; time 0.232  LINCS warning  ralative constraint deviation
after LINCS:
   rms 0.168368,
max 4.765960 (between atoms 858 and 856)
   bonds that
rotated more than 30 degrees:

t=0.232ps : water molecular starting at atom 17660 can not be
settled.
check for bad contact and/or reduce the timestep.
   then the warning happened every step untill the programm crashed.
  Thanks for your discussion!!
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Re: [gmx-users] What can I to do with the problem: lincs warning and water can not be settled?

2009-06-19 Thread Mark Abraham 

xiao shijun wrote:

hi,
  The simulation was OK. But when I changed the epsilon of some atoms to 
get rid of LJ, lincs warning emerged as:
step 116 ; time 0.232  LINCS warning  ralative constraint 
deviation after LINCS:
   rms 
0.168368,  max 4.765960 (between atoms 858 and 856)
   bonds that 
rotated more than 30 degrees:
 
t=0.232ps : water molecular starting at atom 17660 can not be 
settled.

check for bad contact and/or reduce the timestep.
   then the warning happened every step untill the programm crashed.
  Thanks for your discussion!!


See 
http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings


You unbalanced your forcefield, so it's no surprise that it doesn't work 
correctly any more.


Mark
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