nahren manuel wrote:
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.
Did you switch your thermostat between NPT and production MD? The Xi-* terms
are specific to the Nose-Hoover thermostat, so if you used, i.e. Berendsen
during NPT, these terms will not have been written to the .edr file.
You should, however, be able to use a checkpoint file (grompp -t *.cpt) to do
the continuation.
-Justin
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
