GROMACS version:2020_2
GROMACS modification: No
I have a problem I have a simulation, but I lost my .cpt file and .edr file. I don’t have my .cpt file from 500 ns (but I have .cpt file from 400 ns), I try to rerun from 400 ns, but it gives my a little bit different final structure, because I don’t compute on the same computer, so I want to try rerun from 500 ns last frame, with .trr file in which I have velocities, forces and energies. Is it possible and how to do it? What should I do?
Hello,
you can call grompp with your trajectory as input with the -t [.trrfile] flag, along with the rest of your parameters. This generates a .tpr file with the last frame from the trajectory as a starting point (unless you generate new velocities in your .mdp file).
Regards,
Petter
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pjohansson thank you so much for responding. I try but it is not working.
I don’t know why it is not working.
I call grompp
gmx grompp -f eq2.mdp -c MGDG_last_frame_500ns.gro -t eq2.part0006.trr -p system_mgdg.top -o eq2_continuation.tpr
Then in my terminal I have
:-) GROMACS - gmx grompp, 2020.2 (-:
GROMACS: gmx grompp, version 2020.2
Executable: /usr/local/gromacs2020_2/bin/gmx
Data prefix: /usr/local/gromacs2020_2
Working dir: /media/jakub/Maxtor1/MGDG_trzy_warstwy_15_11_2020/400_500ns
Command line:
gmx grompp -f eq2.mdp -c MGDG_last_frame_500ns.gro -t eq2.part0006.trr -p system_mgdg.top -o eq2_continuation.tpr
Ignoring obsolete mdp entry ‘title’
Ignoring obsolete mdp entry ‘cpp’
Ignoring obsolete mdp entry ‘ns_type’
Replacing old mdp entry ‘nstxtcout’ by ‘nstxout-compressed’
NOTE 1 [file eq2.mdp]:
leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
Setting the LD random seed to -304252109
Generated 190 of the 190 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 190 of the 190 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘mgdg’
turning H bonds into constraints…
Excluding 2 bonded neighbours molecule type ‘SOL’
turning H bonds into constraints…
Analysing residue names:
There are: 32400 Other residues
There are: 121500 Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…
Number of degrees of freedom in T-Coupling group Water is 728999.31
Number of degrees of freedom in T-Coupling group non-Water is 2535297.75
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 353 K
Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm
Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory
trr version: GMX_trn_file (single precision)
Last frame 100 time 500000.000
Using frame at t = 500000 ps
Starting time for run is 0 ps
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 256x384x160, spacing 0.095 0.099 0.097
Estimate for the relative computational load of the PME mesh part: 0.35
NOTE 2 [file eq2.mdp]:
This run will generate roughly 1708892 Mb of data
There were 2 notes
Back Off! I just backed up eq2_continuation.tpr to ./#eq2_continuation.tpr.15#
GROMACS reminds you: “But I always say, one’s company, two’s a crowd, and three’s a party.” (Andy Warhol)
This is my mdp file
title = MD equilibration;
tinit = 0
cpp = /lib/cpp ;
constraints = hbonds
constraint_algorithm = lincs ;
integrator = md
dt = 0.002 ;
nsteps = 250500000 ;
nstcomm = 100 ;
comm_mode = linear
continuation = yes ;
; output
nstxout = 500000 ;
nstvout = 500000 ;
nstxtcout = 1000 ;
nstfout = 500000 ;
nstlog = 1000 ;
nstenergy = 1000 ;
nstcalcenergy = 100
cutoff-scheme = Verlet
;
ns_type = grid
nstlist = 10 ;
pbc = xyz
coulombtype = PME
rvdw = 1.0 ;
rlist = 1.0
rcoulomb = 1.0
fourierspacing = 0.1 ;
pme_order = 5 ;
ewald_rtol = 1e-5
; temperature coupling
tcoupl = nose-hoover
tc-grps = water non-water
tau_t = 0.5 0.5 ;
ref_t = 353 353
; pressure
Pcoupl = parrinello-rahman ; parrinello-rahman/no/berendsen
Pcoupltype = anisotropic ;
tau_p = 5.0
compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0
ref_p = 1 1 1 0.0 0.0 0.0
;
When I start mdrun I have
starting mdrun ‘450 mgdg molecules in water’
250500000 steps, 501000.0 ps.
step 0
starting mdrun ‘450 mgdg molecules in water’
250500000 steps, 501000.0 ps.
step 0
It seems to me like it works. It picks up the last frame here:
If you want t0 (which is independent of -t) to be 500ns you need to modify the init-step variable to match it.
Petter
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Thank you so much!