[gmx-users] Make an index file

[Mark Abraham]

On 29/04/2012 7:32 PM, Shima Arasteh wrote:
> Actually, I am confused somehow.
> I want to equilibrate the system. It contains popc and water. To 
> equilibrate it, using .mdp file I use the nvt.mdp file as below.
>
> title        = NVT equilibration for POPC
> define        = -DPOSRES    ; position restrain the protein
> ; Run parameters
> integrator    = md        ; leap-frog integrator
> nsteps        = 50000        ; 2 * 50000 = 100 ps
> dt            = 0.002        ; 2 fs
> ; Output control
> nstxout        = 100        ; save coordinates every 0.2 ps
> nstvout        = 100        ; save velocities every 0.2 ps
> nstenergy    = 100        ; save energies every 0.2 ps
> nstlog        = 100        ; update log file every 0.2 ps
> ; Bond parameters
> continuation    = no            ; first dynamics run
> constraint_algorithm = lincs    ; holonomic constraints
> constraints    = all-bonds            ; all bonds (even heavy atom-H 
> bonds) constrained
> lincs_iter    = 1                    ; accuracy of LINCS
> lincs_order    = 4                    ; also related to accuracy
> ; Neighborsearching
> ns_type        = grid        ; search neighboring grid cels
> nstlist        = 5            ; 10 fs
> rlist        = 1.2        ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 1.2        ; short-range electrostatic cutoff (in nm)
> rvdw        = 1.2        ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype    = PME        ; Particle Mesh Ewald for long-range 
> electrostatics
> pme_order    = 4            ; cubic interpolation
> fourierspacing    = 0.16        ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl        = V-rescale                ; modified Berendsen thermostat
> tc-grps        = POPC SOL    ; two coupling groups - more accurate

Here you instruct grompp to expect the POPC group...

> tau_t        = 0.1    0.1                ; time constant, in ps
> ref_t        = 323     323                ; reference temperature, one 
> for each group, in K
> ; Pressure coupling is off
> pcoupl        = no         ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc            = xyz        ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres    ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel        = yes        ; assign velocities from Maxwell distribution
> gen_temp    = 323        ; temperature for Maxwell distribution
> gen_seed    = -1        ; generate a random seed
>
>
>
> I enter this command:
> # grompp -f nvt.mdp -c em.gro -p popc.top -o nvt.tpr
>
> Getting this fatal error:
> Group POPC not found in 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 don't need index file, do I?  What is the problem with my .mdp file?

... but POPC is not defined implicitly by your .top+.gro combination, 
nor explicitly in an index file supplied with grompp -n. AFAIK if your 
[moleculetype] is named POPC then it is all OK, but maybe the fact that 
your .gro file has the POPC "residues" named POP is confusing that 
mechanism. As you can see with your earlier example with make_ndx, the 
POP group is defined implicitly by the residue names in your .gro file, 
so if you use that output index file and reference POP in your .mdp 
file, all will be good. You might get away without using that index 
file, but I am not sure about this. Simpler still is to use Water and 
non-Water as your T-coupling groups, but this will need changing if down 
the road you need Protein as well (or such).

Mark
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