[gmx-users] Umbrella Sampling gromacs 5.0 error

[Justin Lemkul]

On 11/17/14 11:02 PM, Alexander Law wrote:
> Dear vmx-users
>
> I am running through Dr Lemkul's umbrella sampling tutorial and applying this to my own structure. I have problem with the pull simulation command: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr
>
> I receive this error message back:
>
>
> Ignoring obsolete mdp entry 'title'
>
> Ignoring obsolete mdp entry 'optimize_fft'
>
> Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
>
> ERROR: pull-coord1-groups should have 2 components
>
>
> WARNING 1 [file md_pull.mdp, line 62]:
>
>    Unknown left-hand 'pull-group0' in parameter file
>
>
>
>
> WARNING 2 [file md_pull.mdp, line 62]:
>
>    Unknown left-hand 'pull-group1' in parameter file
>
>
>
>
> WARNING 3 [file md_pull.mdp, line 62]:
>
>    Unknown left-hand 'pull_rate1' in parameter file
>
>
>
>
> WARNING 4 [file md_pull.mdp, line 62]:
>
>    Unknown left-hand 'pull_k1' in parameter file
>
>
>
>
> NOTE 2 [file md_pull.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 md_pull.mdp]:
>
>    nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
>
>    nstcomm to nstcalcenergy
>
>
>
> NOTE 4 [file md_pull.mdp]:
>
>    leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
>
>
> ------------------------------
>
> Fatal error:
>
> Group Protein referenced in the .mdp file was not found in the index file.
>
> Group names must match either [moleculetype] names or custom index group
>
> names, in which case you must supply an index file to the '-n' option
>
> of grompp.
>
>
> My Index file is set up properly, with force being applied to Chain_A, and Chain_B is my static reference:
>
> 0 Chain_B             :  1290 atoms
>
> 1 Chain_A             :   110 atoms
>

The fatal error is due to the fact that you've deleted the other necessary 
groups.  You should add Chain_A and Chain_B to an index file, but not delete the 
other groups.

>
> The md_pull.mdp remains the same:
>
>
> ; Pull code
>
> pull            = umbrella
>
> pull_geometry   = distance  ; simple distance increase
>
> pull_dim        = N N Y
>
> pull_start      = yes       ; define initial COM distance > 0
>
> pull_ngroups    = 1
>
> pull_group0     = Chain_B
>
> pull_group1     = Chain_A
>
> pull_rate1      = 0.01      ; 0.01 nm per ps = 10 nm per ns
>
> pull_k1         = 1000      ; kJ mol^-1 nm^-2
>
>
> Any advice on how to treat this problem is appreciated.
>

Regarding the .mdp keywords, note from the first page of the tutorial:

"PLEASE NOTE: This tutorial has NOT been updated to reflect the new selection 
syntax and .mdp options introduced in GROMACS 5.0."

Use an older version (4.6.x) or check the manual for the new syntax; it doesn't 
differ much.  I just haven't had the chance to make the changes and verify that 
things still work as expected.

-Justin

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

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

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