[gmx-users] Umbrella Sampling Error in Gromacs 5.0

[Justin Lemkul]

On 4/22/15 3:54 PM, Jianhui Tian wrote:
> 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
> ########################################################

Something is messed up in the input coordinates.  If the reference distance is 
"not a number," then you need to diagnose what it is you've done to the 
coordinates before doing anything else.

-Justin

> 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.
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================