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