subject:"\[gmx\-users\] MD simulation error \: rRNA simulaion"

Re: [gmx-users] MD simulation error : rRNA simulaion

2017-10-05 Thread 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 
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  = 5 ; 2 * 5 = 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
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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>
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[gmx-users] MD simulation error : rRNA simulaion

2017-10-05 Thread Hemant Arya

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  = 5 ; 2 * 5 = 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
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] MD simulation error : rRNA simulaion

[gmx-users] MD simulation error : rRNA simulaion

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