[gmx-users] Equilibriation nvt.mdp error

[Tsjerk Wassenaar]

Hi Wholly,

It would be better to install a more recent version of gromacs. The
tutorial should state which version it is written for.

Cheers,

Tsjerk

On Mar 17, 2012 9:01 AM, "Wholly Peach" <whollypeach at yahoo.com> wrote:

Dear All,

I am running the on-line tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html
.

By "grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr", with the nvt.mdp
downloaded as attached following, I got the following error message:

"
creating statusfile for 1 node...
ERROR: invalid enum 'V-rescale' for variable tcoupl, using 'No'
Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes' 'Andersen'
'Andersen-interval'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.14#
WARNING 1 [file nvt.mdp, line unknown]:
 Unknown left-hand 'continuation' in parameter file
checking input for internal consistency...
calling cpp...
processing topology...
Generated 165 of the 1596 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
turning all bonds into constraints...
Excluding 2 bonded neighbours for SOL 10242
turning all bonds into constraints...
Excluding 1 bonded neighbours for NA+ 0
turning all bonds into constraints...
Excluding 1 bonded neighbours for CL- 8
turning all bonds into constraints...
processing coordinates...
double-checking input for internal consistency...
WARNING 2 [file "topol.top", line 8274]:
 For energy conservation with LINCS, lincs_iter should be 2 or larger.
 You can safely ignore this if your system doesn't have any
 LINCS-constrained bonds;
 for water molecules we normally use the analytical SETTLE algorithm
 instead.
Setting gen_seed to 978754
Velocities were taken from a Maxwell distribution at 300 K
There were 2 warnings
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 1109
Fatal error:
There were 1 error(s) processing your input
-------------------------------------------------------

"

I am looking forward to getting a message on what is the problem.

Cheers,
Wholly



nvt.mdp:

title  = OPLS Lysozyme NVT equilibration
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 cells
nstlist  = 5  ; 10 fs
rlist  = 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)
; 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  = 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 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 = 300  ; temperature for Maxwell distribution
gen_seed = -1  ; generate a random seed




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