[gmx-users] umbrella sampling error

[Justin Lemkul]

On 1/5/16 5:36 AM, Nikhil Maroli wrote:
> Dear all,
> im running umbrella sampling when invoke the following command i got the
> follwoing warnings and grompp terminated becasue of so much warning
> ,initially i neutralised the My protein-Ligand system with NACl,so how come
> there will be a charge?  (NOTE 5)what i can do for that?  can i use maxwarn
> option as im running equilibration?
>

Well, simply put, you did something wrong because you still have a net charge of 
-12 (ignore the floating-point difference here, it's actually -12).

Don't use -maxwarn to simply overcome something inconvenient, though in this 
case its use has no bearing on any notes and only affects the warning, which you 
should heed; your selected method is not necessarily stable under the conditions 
specified.

-Justin

>    gmx grompp -f npt_umbrella.mdp -c conf128.gro -p topol.top -n index.ndx
> -o npt125.tpr
>
>
> NOTE 1 [file npt_umbrella.mdp, line 66]:
>    npt_umbrella.mdp did not specify a value for the .mdp option
>    "cutoff-scheme". Probably it was first intended for use with GROMACS
>    before 4.6. In 4.6, the Verlet scheme was introduced, but the group
>    scheme was still the default. The default is now the Verlet scheme, so
>    you will observe different behaviour.
>
>
>
>
> NOTE 2 [file npt_umbrella.mdp]:
>    With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>    that with the Verlet scheme, nstlist has no effect on the accuracy of
>    your simulation.
>
>
>
> NOTE 3 [file npt_umbrella.mdp]:
>    nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
>    nstcomm to nstcalcenergy
>
>
> NOTE 4 [file npt_umbrella.mdp]:
>    leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
>
>
> WARNING 1 [file npt_umbrella.mdp]:
>    You are generating velocities so I am assuming you are equilibrating a
>    system. You are using Parrinello-Rahman pressure coupling, but this can
>    be unstable for equilibration. If your system crashes, try equilibrating
>    first with Berendsen pressure coupling. If you are not equilibrating the
>    system, you can probably ignore this warning.
>
>
>
>
>
> *NOTE 5 [file topol.top, line 77254]:*
> *  System has non-zero total charge: -11.999994*
> *  Total charge should normally be an integer. See*
> *  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> <http://www.gromacs.org/Documentation/Floating_Point_Arithmetic>*
> *  for discussion on how close it should be to an integer.*
>
>
>
>
> Setting gen_seed to 2839808349
> Velocities were taken from a Maxwell distribution at 310 K
> Removing all charge groups because cutoff-scheme=Verlet
> Pull group 1 'Chain_A' has 8120 atoms
> Pull group 2 'Chain_B' has 33 atoms
> Number of degrees of freedom in T-Coupling group Protein is 16109.61
> Number of degrees of freedom in T-Coupling group non-Protein is 108398.39
> Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K
> Calculated rlist for 1x1 atom pair-list as 1.408 nm, buffer size 0.008 nm
> Set rlist, assuming 4x4 atom pair-list, to 1.400 nm, buffer size 0.000 nm
> Note that mdrun will redetermine rlist based on the actual pair-list setup
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 72x56x104, spacing 0.111 0.116 0.116
> Pull group  natoms  pbc atom  distance at start  reference at t=0
>         1      8120      4060
>         2        33      8137       1.117 nm          1.117 nm
> Estimate for the relative computational load of the PME mesh part: 0.10
> This run will generate roughly 32 Mb of data
>
> There were 5 notes
>
> There was 1 warning
>
> -------------------------------------------------------
> Program gmx grompp, VERSION 5.1
> Source code file:
> /home/user/gromacs-5.1/src/gromacs/gmxpreprocess/grompp.c, line: 2107
>
> Fatal error:
> Too many warnings (1), gmx terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>

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

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

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