[gmx-users] continue Prod run from NPT eq

[Justin A. Lemkul]

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
> 
> 

-- 
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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

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