[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
Anna Duncan
anna.duncan at mrc-mbu.cam.ac.uk
Thu Jun 2 20:39:05 CEST 2011
Hi Justin,
Thanks for your speedy response. I've set off the simulation with the
checkpoint file rather than the trajectory and energy files and that
seems to be going fine now.
v4.5.3 g_energy showed the .edr file from the backbone-restrained run
to have no Xi-0-Protein term present, although the .edr file from the
equilibration run has a term called 'Xi-Protein'
Best wishes,
Anna
On 2 Jun 2011, at 18:36, Justin A. Lemkul wrote:
>
>
> 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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