[gmx-users] Umbrella Sampling gromacs 5.0 error

Alexander Law alexander.law at pg.canterbury.ac.nz
Tue Nov 18 05:03:00 CET 2014

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 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.



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