[gmx-users] Umbrella Sampling Error in Gromacs 5.0

[Jianhui Tian]

Dear Users,

I am trying to do a umbrella pulling of one lipid out of a bilayer using
umbrella sampling code. In Gromacs 5.0, there is a big change in umbrella
sampling implementation. I set my pull parameters like this:

pull             = umbrella
pull_geometry   = cylinder  ; Pull in the direction of pull-vec.
pull_coord1_vec = 0.0 0.0 -1.0
pull_r1 = 1.0
pull_r0 = 1.5
pull_start = yes
pull_ngroups = 2
pull_ncoords = 1
pull_coord1_groups     = 1 2
pull_group1_name     = PullLipid  ; one lipid that I want to pull out
pull_group2_name        = RefLipids   ; lipids on the other leaflet of
bilayer
pull_coord1_rate = 0.001 ; 0.001 nm per ps = 1 nm per ns
pull_coord1_k         = 1000      ; kJ mol^-1 nm^-2

When I have a small system, it can work but had and following error and
stopped:

Fatal error:
Distance between pull groups 1 and 2 (2.707004 nm) is larger than 0.49
times the box size (2.758373).
You might want to consider using "pull-geometry = direction-periodic"
instead.

I guess this is due to a small box size (about 5.52 nm in x and y).

Then I double the system size and redo the umbrella sampling. I got the
following message with grompp:
########################################################
Pull group  natoms  pbc atom  distance at start     reference at t=0
       1       130     23335
       2      3136     38129    -nan    -nan
########################################################
The tpr file was generated without problem.

Then, I tried to do a MD run and the job crashed with the energy terms in
the log file like this:
########################################################
          Step           Time         Lambda
              0        0.00000        0.00000

   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
    2.31656e+04    1.35314e+05    8.06516e+04    9.35503e+02    1.09158e+04
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.   COM Pull En.
   -1.90682e+05   -6.69381e+02   -8.45045e+05    4.84404e+03           -nan
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
           -nan           -nan           -nan           -nan           -nan
   Constr. rmsd
            nan
########################################################

Does anyone experience similar problem before? Any hint is welcomed. Thanks
for your attention and help.

J.