[gmx-users] continue Prod run from NPT eq

[Justin A. Lemkul]

manu.mura wrote:
> 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'
> ---------------------------------------------------------------
> 

I think this is related to a bug that was recently solved, regarding the 
inability to read double-precision energy files.

A new release, 4.5.3, will be released soon, as this bug is fairly significant.

-Justin

> 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
> 

-- 
========================================

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

========================================