[gmx-users] Re: freeze the particular residues in NPT-NVT

[Justin Lemkul]

On Wed, Mar 20, 2013 at 9:40 AM, 라지브간디 <rajiv at kaist.ac.kr> wrote:

>
> p{margin:0;padding:0;}
>
>
> Thanks for your mail Justin.
>
>
> I encountered the another problem after i didn't delete the whole part
> (protein, system, non-prptein..etc) in index.ndx file.
>
>
> Fatal error:
> 37872 atoms are not part of any of the T-Coupling groups
>
>
Usually the "Protein Non-Protein" approach covers everything. Apparently in
your case, something is wrong and you will have to figure out what has not
been accounted for. Try using gmxcheck on your index file to see if there
is a group (or groups) whose contents account for 37872 atoms.

-Justin


> These are my NVT.mdp file :
> title                   = OPLS Lysozyme NVT equilibration define
>      = -DPOSRES      ; position restrain the protein; Run
> parametersintegrator       = md            ; leap-frog integratornsteps
>        = 50000         ; 2 * 50000 = 100 psdt          = 0.002         ; 2
> fs; Output controlnstxout           = 100           ; save coordinates
> every 0.2 psnstvout          = 100           ; save velocities every 0.2
> psnstenergy = 100           ; save energies every 0.2 psnstlog
>  = 100           ; update log file every 0.2 ps; Bond
> parameterscontinuation     = no            ; first dynamics
> runconstraint_algorithm = lincs        ; holonomic constraints constraints
>     = all-bonds     ; all bonds (even heavy atom-H bonds)
> constrainedlincs_iter     = 1             ; accuracy of LINCSlincs_order  =
> 4             ; also related to accuracy; Neighborsearchingns_type
>    = grid          ; search neighboring grid cellsnstlist          = 5
>         ; 10 fsrlist            = 1.0           ; short-range neighborlist
> cutoff (in nm)rcoulomb       = 1.0           ; short-range electrostatic
> cutoff (in nm)rvdw          = 1.0           ; short-range van der Waals
> cutoff (in nm); Electrostaticscoulombtype   = PME           ; Particle Mesh
> Ewald for long-range electrostaticspme_order    = 4             ; cubic
> interpolationfourierspacing     = 0.16          ; grid spacing for FFT;
> Temperature coupling is ontcoupl                = V-rescale     ; modified
> Berendsen thermostattc-grps          = Protein Non-Protein   ; two coupling
> groups - more accuratetau_t              = 0.1 0.1               ; time
> constant, in psref_t             = 300 300               ; reference
> temperature, one for each group, in K; Pressure coupling is offpcoupl
>         = no            ; no pressure coupling in NVT; Periodic boundary
> conditionspbc          = xyz           ; 3-D PBC; Dispersion
> correctionDispCorr        = EnerPres      ; account for cut-off vdW scheme;
> Velocity generationgen_vel            = yes           ; assign velocities
> from Maxwell distributiongen_temp   = 300           ; temperature for
> Maxwell distributiongen_seed  = -1            ; generate a random
> seedfreezegrps      = g1 g2 g3 g4 g5 g6 g7 g8 g9 g10 g11 g12 g13 g14 g15
> g16 g17 g18 g19 g20 g21 g22 g23 g24 g25 g26 g27 g28 g29    freezedim
> =  Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y
> Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y
> Y Y Y Y Y Y Y Y Y Y Y Y Y
>
>
>
>
>
>
> > Dear gmx,
> >
> >
> > I have used freezgreps for 20 residues of 152 residues contained protein
> > and the it took well for energy minimization steps according to the input
> > given on mdp and index files. However, when i go for further NPT steps it
> > gives following error.
> >
> >
> > 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.
> >
> >
> > I have rechecked the reference structure (em.gro) with index and nvt.mdp
> > files but all of their index numbers are correct. can anyone tell me how
> > would avoid them? Thanks in advance.
> >
> >
> The "Protein" group is a default group and should always be present. The
> only reason I can think of that would cause this is if you created an index
> file and then deleted the Protein group from it. If grompp receives an
> index file on the command line, the groups provided therein supersede
> default groups.
>
>
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-- 

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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