[gmx-users] Switching from v4.0.7 to v 4.5.3 - being able to get the correct terms from a edr file when continuing a simulation
Justin A. Lemkul
jalemkul at vt.edu
Thu Jun 2 19:36:57 CEST 2011
Anna Duncan wrote:
>
> Hi,
>
> I'm doing a coarse-grained simulation, using the MARTINI forcefield, of
> a protein in a lipid bilayer. I carried out the equilibration stages
> using Gromacs 4.0.7. Equilibration was done in several stages but the
> last stage was with a Nosé-Hoover thermostat for temperature coupling
> and Parrinello-Rahman thermostat for pressure coupling. The next stage
> I carried out was a simulation of system with nothing except the
> backbone of the protein restrained, to relax the sidechains. For this
> stage I used a newer, faster server which has Gromacs 4.5.3 installed on
> it. The mdp file is below.
> I used the command:
> g_grompp -f ../md_T296.mdp -p ../prot_memb_system2.top -c npt_bPR.gro -e
> npt_bPR.edr -t npt_bPR.trr -n prot_bilayer.ndx -o md_schain
>
> I got the error message:
> -------------------------------------------------------
> Program g_grompp, VERSION 4.5.3
> Source code file:
> /builddir/build/BUILD/gromacs-4.5.3/src/gmxlib/enxio.c, line: 1056
>
> 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 assumed that this was something to do with my switching between
> versions, maybe that the .edr file that's written by version 4.0.7
> doesn't have the terms that are required by version 4.5.3, so I removed
> the -e option from the command line and ran the simulation using the
> commands:
> g_grompp -f ../md_T296.mdp -p ../prot_memb_system2.top -c npt_bPR.gro -t
> npt_bPR.trr -n prot_bilayer.ndx -o md_schain
> g_mdrun -v -nt 1 -deffnm md_schain
>
> For the next stage, I want to simulate the whole system, for which I use
> the mdp file below except with no -DPOSREBB defined (line 10) and with
> nsteps = 10000000, and version 4.5.3 again.
> When I use the command:
> g_grompp -f ../md_T296.mdp -p ../prot_memb_system2.top -c md_schain.gro
> -e md_schain.edr -t md_schain.trr -n prot_bilayer.ndx -o md1_t296
>
> I again get the error message:
> -------------------------------------------------------
> Program g_grompp, VERSION 4.5.3
> Source code file:
> /builddir/build/BUILD/gromacs-4.5.3/src/gmxlib/enxio.c, line: 1056
>
> 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
> -------------------------------------------------------
>
What does g_energy tell you is in the .edr file? If g_energy says Xi-0-Protein
is present, but grompp can't find it, then perhaps there's a grompp-specific
problem reading the energy file. It would also be interesting to know if the
problem persists in 4.5.4, as I know there has been some debugging of .edr
files, but I can't find anything specific in the release history that might be
pertinent here.
>
> Can you help me with exactly what's going wrong? I'm not sure if I
> should be carrying out the simulation without being able to pass on the
> information from the .edr file of the sidechain-relaxing simulation? If
> not, what can I do to pass on the information necessary from the .edr file?
>
Forget about passing .trr and .edr files to grompp. It's more accurate to
simply pass a checkpoint file to grompp -t. Checkpoints contain all the
necessary state information for the system.
-Justin
> Many thanks in advance,
>
> Anna
>
> ***********************************************************
> mdp file
> ***********************************************************
> ;
> ; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0
> ;
> ; for use with GROMACS 3.3
> ;
>
> ; VARIOUS PREPROCESSING OPTIONS =
> title = Martini
> cpp = /usr/bin/cpp
> define = -DPOSREBB
>
> ; RUN CONTROL PARAMETERS =
> ; MARTINI - Most simulations are stable with dt=40 fs,
> ; some (especially rings) require 20-30 fs.
> ; The range of time steps used for parametrization
> ; is 20-40 fs, using smaller time steps is therefore not recommended.
>
> integrator = md
> ; start time and timestep in ps
> tinit = 0.0
> dt = 0.030
> nsteps = 1000000
> ; number of steps for center of mass motion removal =
> nstcomm = 1
> comm-mode = Linear
> comm-grps = Protein_Lipids W
>
> ; OUTPUT CONTROL OPTIONS =
> ; Output frequency for coords (x), velocities (v) and forces (f) =
> nstxout = 5000
> nstvout = 5000
> nstfout = 0
> ; Output frequency for energies to log file and energy file =
> nstlog = 1000
> nstenergy = 1000
> ; Output frequency and precision for xtc file =
> nstxtcout = 1000
> xtc_precision = 100
> ; This selects the subset of atoms for the xtc file. You can =
> ; select multiple groups. By default all atoms will be written. =
> xtc-grps =
> ; Selection of energy groups =
> energygrps =
>
> ; NEIGHBORSEARCHING PARAMETERS =
> ; MARTINI - no need for more frequent updates
> ; or larger neighborlist cut-off due
> ; to the use of shifted potential energy functions.
>
> ; nblist update frequency =
> nstlist = 10
> ; ns algorithm (simple or grid) =
> ns_type = grid
> ; Periodic boundary conditions: xyz or none =
> pbc = xyz
> ; nblist cut-off =
> rlist = 1.2
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW =
> ; MARTINI - vdw and electrostatic interactions are used
> ; in their shifted forms. Changing to other types of
> ; electrostatics will affect the general performance of
> ; the model.
>
> ; Method for doing electrostatics =
> coulombtype = Shift
> rcoulomb_switch = 0.0
> rcoulomb = 1.2
> ; Dielectric constant (DC) for cut-off or DC of reaction field =
> epsilon_r = 15
> ; Method for doing Van der Waals =
> vdw_type = Shift
> ; cut-off lengths =
> rvdw_switch = 0.9
> rvdw = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure =
> DispCorr = No
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
> ; MARTINI - normal temperature and pressure coupling schemes
> ; can be used. It is recommended to couple individual groups
> ; in your system seperately.
>
> ; Temperature coupling =
> tcoupl = Nose-Hoover
> nsttcouple = 1
> ; Groups to couple separately =
> tc-grps = Protein W Lipids
> ; Time constant (ps) and reference temperature (K) =
> tau_t = 1.2 1.2 1.2
> ref_t = 296 296 296
> ; Pressure coupling =
> Pcoupl = Parrinello-Rahman
> Pcoupltype = semiisotropic
> nstpcouple = 1
> ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
> tau_p = 12.0
> compressibility = 3e-5 3e-5
> ref_p = 1.0 1.0
>
> ; GENERATE VELOCITIES FOR STARTUP RUN =
> gen_vel = no
> gen_temp = 296
> gen_seed = 666
>
> ; Distance restraints type: No, Simple or Ensemble
> disre = Simple
> ; Force weighting of pairs in one distance restraint: Conservative or Equal
> disre-weighting = Conservative
> ; Use sqrt of the time averaged times the instantaneous violation
> disre-mixed = no
> disre-fc = 500
> disre-tau = 0
> ; Output frequency for pair distances to energy file
> nstdisreout = 100
>
> ; OPTIONS FOR BONDS =
> ; MARTINI - for ring systems constraints are defined
> ; which are best handled using Lincs.
>
>
> constraints = none
> ; Type of constraint algorithm =
> constraint_algorithm = Lincs
> ; Do not constrain the start configuration =
> unconstrained_start = yes
> ; Highest order in the expansion of the constraint coupling matrix =
> lincs_order = 4
> ; Lincs will write a warning to the stderr if in one step a bond =
> ; rotates over more degrees than =
> lincs_warnangle = 30
>
> ; FREEZE GROUPS
> freezegrps =
> freezedim =
>
> ; CONTINUATION
> ; this is specified by using -t -e flags in grompp and
> unconstrained_start = yes
>
--
========================================
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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