[gmx-users] Umbrella Sampling Error in Gromacs 5.0

[Jianhui Tian]

>
> Date: Wed, 22 Apr 2015 16:05:18 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Umbrella Sampling Error in Gromacs 5.0
> Message-ID: <5537FEFE.6020300 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> 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
>

Thanks, Justin.

But, what do you mean by coordinates messed up?
I have a gro file for generating the tpr for umbrella pulling.
The same GRO file can be used to generate a tpr file for normal MD run
without any problems.

Best,
J.



>
> > 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
>
>