[gmx-users] MD simulation error : rRNA simulaion

[Tasneem Kausar]

In energy group you have given Potein and non-Protein and you are not
simulation a protein but RNA.

On Fri, Oct 6, 2017 at 12:53 AM, Hemant Arya <arya.hemant2009 at gmail.com>
wrote:

> Dear gromacs,
> Greetings
> I am trying to run a NVT with the following command.
>
> My mdp file is below
>
> title       = Protein-ligand complex NVT equilibration
> define      = -DPOSRES  ; position restrain the protein and ligand
> ; Run parameters
> integrator  = md        ; leap-frog integrator
> nsteps      = 50000     ; 2 * 50000 = 100 ps
> dt          = 0.002     ; 2 fs
> ; Output control
> nstxout     = 500       ; save coordinates every 0.2 ps
> nstvout     = 500       ; save velocities every 0.2 ps
> nstenergy   = 500       ; save energies every 0.2 ps
> nstlog      = 500       ; update log file every 0.2 ps
> energygrps  = Protein Non-protein
> ; 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
> cutoff-scheme   = Verlet
> ns_type     = grid      ; search neighboring grid cells
> nstlist     = 10         ; 10 fs
> *rcoulomb    = 1.0       ; short-range electrostatic cutoff (in nm)*
> *rvdw        = 1.4       ; 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
> tcoupl      = V-rescale                     ; modified Berendsen thermostat
> tc_grps = Protein Non-Protein    ; two coupling groups - more accurate
> tau_t       = 0.1   0.1                     ; time constant, in ps
> ref_t       = 300   300                     ; reference temperature, one
> for each group, in K
> ; Pressure coupling
> 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    = 300       ; temperature for Maxwell distribution
> gen_seed    = -1        ; generate a random seed
>
>
>
> Error :
>
> GROMACS:      gmx grompp, VERSION 5.1.4
> Executable:   /home/amouda/Desktop/gromacs-5.1.4/build/bin/gmx
> Data prefix:  /home/amouda/Desktop/gromacs-5.1.4 (source tree)
> Command line:
>   gmx grompp -f nvt.mdp -c em-steep.gro -p trp.top -o pr-nvt.tpr -n
> index.ndx
>
> Ignoring obsolete mdp entry 'title'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.17#
>
> *ERROR 1 [file nvt.mdp]:*
> *  With Verlet lists rcoulomb!=rvdw is not supported*
>
> Setting the LD random seed to 2859163501
> Generated 20503 of the 20503 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 17396 of the 20503 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'RNA_chain_1'
> turning all bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'NA'
> turning all bonds into constraints...
> Setting gen_seed to 1604041440
> Velocities were taken from a Maxwell distribution at 300 K
> Removing all charge groups because cutoff-scheme=Verlet
>
>
> When i gave equal parameter to coulomb (1.4) and rvdw (1.4) then it shows
> different error
> like
> "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."
>
>
> Please help me to solve the problem.
> Thanks
> --
> *Hemant Arya*
> Research Scholar
> UGC-RGNF
> Centre for Bioinformatics,
> School of Life Sciences,
> Pondicherry University
> Kalapet
> Puducherry- 605014
> INDIA
> Contact No. +91 9597221248
>                    +91 2930-244141
> --
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