VMD-L Mailing List

From: Naiyin Yu (nyyu_at_brandeis.edu)
Date: Wed Jan 13 2010 - 21:44:03 CST

Dear All,

I am trying to use "colvar" to constrain the distance between two
monomers when I equilibrate the system before the simulation. The
problem is after heating to the certain temperature (step by step),
the system started to equilibrate with harmonic constraint on the two
monomers. While it failed at the first step and the namd output
showed like:

ERROR: Atom 35 velocity is nan nan nan (limit is 6000)
...
...

and the error file gave the following message:

------------ Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Periodic cell has become too small for original
patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.

I have already enlarge the margin or change the forceConstant but
nothing new happened. Does anyone know what's the problem?

Here is the script I use:

colvar {
         name com
         width 2.5
         outputSystemForce off
         outputAppliedForce on

         distance {

                 group1 {
                          atomsFile Acom.pdb
                          atomsCol O
                          atomsColValue 2.0
                  }

                 group2 {
                                  atomsFile Bcom.pdb
                                  atomsCol O
                                  atomsColValue 2.0
                  }
         }
}

harmonic {
         colvars com
         forceConstant 0.1
         centers 24
}