[gmx-users] continue Prod run from NPT eq

[nahren manuel]

Dear Gromacs Users,

I am using ver 4.5.1.

I completed a 500 ps run of NPT (the mdp file is below). after when i try to do a prod run with both velocity and pressure read from the output of NPT, I get a error

newgrompp -f eq3npt.mdp -o eq3npttpr.tpr -p dimertop.top -c eq2nptpdb.pdb -t eq2npttrr.trr -e eq2nptedr.edr

**********
     

READ 3 BOX VELOCITIES FROM eq2nptedr.edr


-------------------------------------------------------
Program newgrompp, 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 cannot judge where I go wrong. Kindly help.

Best,
nahren

***********

****  mdp file  *******

define        = -DPOSRES    ; position restrain the protein
; Run parameters
integrator    = md        ; leap-frog integrator
nsteps        = 250000        ; 2 * 250000 = 500 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    = 250        ; save energies every 0.2 ps
nstlog        = 500        ; update log file every 0.2 ps
; Bond parameters
continuation    = yes        ; 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        = 1.0        ; short-range neighborlist cutoff (in nm)
rcoulomb    = 1.5        ; short-range electrostatic cutoff (in nm)
rvdw        = 1.0        ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype    = cut-off        ; Particle Mesh Ewald for long-range electrostatics
;
; Temperature coupling is on
tcoupl        = Nose-Hoover        ; More accurate thermostat
tc-grps        = Protein SOL    ; three coupling groups - more accurate
tau_t        = 0.2    0.2        ; time constant, in ps
ref_t        = 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        = 5.0            ; 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        ; assign velocities from Maxwell distribution
; COM motion removal
; These options remove motion of the protein/bilayer relative to the solvent/ions
nstcomm        = 1
comm-mode    = Linear
comm-grps    = system




      
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