[gmx-users] continue Prod run from NPT eq

[manu.mura]

Dear Justin,
I run again the simulation, this time I keep the same thermostat 
(Nose-Hoover). I still get the same error
manu.mura wrote:
------------------------------------------------------------
READ 3 BOX VELOCITIES FROM final_NPT.edr


-------------------------------------------------------
Program grompp_mpi_d, VERSION 4.5.1
Source code file: enxio.c, line: 1022

Fatal error:
Could not find energy term named 'Xi-0-Protein'
---------------------------------------------------------------

my input file is the following:

; Run parameters
integrator    = md        ; leap-frog integrator
nsteps        = 40000000    ; 2 * 500000 = 1000 ps (1 ns)
dt        = 0.002        ; 2 fs
; Output control
nstxout        = 1000        ; save coordinates every 2 ps
nstvout        = 1000        ; save velocities every 2 ps
nstxtcout    = 1000        ; xtc compressed trajectory output every 2 ps
nstenergy    = 1000        ; save energies every 2 ps
nstlog        = 1000        ; update log file every 2 ps
; Bond parameters
continuation    = yes        ; Restarting after NPT
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        = Nose-Hoover        ; More accurate thermostat
tc-grps        = Protein DMP    SOL    ; three coupling groups - more
accurate
tau_t        = 0.2    0.2    0.2    ; time constant, in ps
ref_t        = 300     300    300    ; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl        = Parrinello-Rahman    ; Pressure coupling on in NPT
pcoupltype    = semiisotropic        ; uniform scaling of x-y box
vectors, independent z
tau_p        = 2.0            ; time constant, in ps
ref_p        = 1.0    1.0        ; reference pressure, x-y, z (in bar)
compressibility = 4.5e-5    4.5e-5    ; isothermal compressibility, bar^-1
; Periodic boundary conditions
pbc        = xyz        ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres    ; account for cut-off vdW scheme
; Velocity generation
gen_vel        = no        ; Velocity generation is off
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm         = 1
comm-mode       = Linear
comm-grps       = Protein_DMP SOL

Thank you
best regards

Manuela

    Dear Justin,
    I have the same problem.
    I started with Berendsen during NPT and I switch the thermostat
    (Nose-Hoover ) to run MD.
    I get the following error.
    Program grompp_mpi_d, VERSION 4.5.1
    Source code file: enxio.c, line: 1022

    Fatal error:
    Could not find energy term named 'Xi-0-Protein'
    For more information and tips for troubleshooting, please check the GROMACS
    website at http://www.gromacs.org/Documentation/Errors
    -------------------------------------------------------
    I am not able to do the checkpoint file ( grompp -t *.cpt) because I get
    another error.
      

Saying that you "get another error" is not helpful. You cannot pass an
.edr file to grompp when switching thermostats. You should be able to
pass a checkpoint file to preserve all velocities, etc. If you want
further help, post the exact error message, and perhaps your .mdp file.
Otherwise, all I can say is either something went wrong or you're doing
something wrong.

-Justin


    Could you help me.
    Thank you

    Best Regards
    Manuela

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101105/dc003df5/attachment.html>