<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div><div>Hi Justin,</div><div><br></div><div>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. </div><div><br></div>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'<div><br></div><div>Best wishes,</div><div><br></div><div>Anna</div><div><br></div><div><br></div><div><br><div><div>On 2 Jun 2011, at 18:36, Justin A. Lemkul wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><br><br>Anna Duncan wrote:<br><blockquote type="cite">Hi,<br></blockquote><blockquote type="cite">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.<br></blockquote><blockquote type="cite">I used the command:<br></blockquote><blockquote type="cite">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<br></blockquote><blockquote type="cite">I got the error message:<br></blockquote><blockquote type="cite">-------------------------------------------------------<br></blockquote><blockquote type="cite">Program g_grompp, VERSION 4.5.3<br></blockquote><blockquote type="cite">Source code file: /builddir/build/BUILD/gromacs-4.5.3/src/gmxlib/enxio.c, line: 1056<br></blockquote><blockquote type="cite">Fatal error:<br></blockquote><blockquote type="cite">Could not find energy term named 'Xi-0-Protein'<br></blockquote><blockquote type="cite">For more information and tips for troubleshooting, please check the GROMACS<br></blockquote><blockquote type="cite">website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br></blockquote><blockquote type="cite">-------------------------------------------------------<br></blockquote><blockquote type="cite">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:<br></blockquote><blockquote type="cite">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<br></blockquote><blockquote type="cite">g_mdrun -v -nt 1 -deffnm md_schain<br></blockquote><blockquote type="cite">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.<br></blockquote><blockquote type="cite">When I use the command:<br></blockquote><blockquote type="cite">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<br></blockquote><blockquote type="cite">I again get the error message:<br></blockquote><blockquote type="cite">-------------------------------------------------------<br></blockquote><blockquote type="cite">Program g_grompp, VERSION 4.5.3<br></blockquote><blockquote type="cite">Source code file: /builddir/build/BUILD/gromacs-4.5.3/src/gmxlib/enxio.c, line: 1056<br></blockquote><blockquote type="cite">Fatal error:<br></blockquote><blockquote type="cite">Could not find energy term named 'Xi-0-Protein'<br></blockquote><blockquote type="cite">For more information and tips for troubleshooting, please check the GROMACS<br></blockquote><blockquote type="cite">website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br></blockquote><blockquote type="cite">-------------------------------------------------------<br></blockquote><br>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.<br><font class="Apple-style-span" color="#000000"><font class="Apple-style-span" color="#144FAE"><br></font></font></div></blockquote><blockquote type="cite"><div><blockquote type="cite">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?<br></blockquote><br>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.<br><br>-Justin<br><br><blockquote type="cite">Many thanks in advance,<br></blockquote><blockquote type="cite">Anna<br></blockquote><blockquote type="cite">***********************************************************<br></blockquote><blockquote type="cite">mdp file<br></blockquote><blockquote type="cite">***********************************************************<br></blockquote><blockquote type="cite">;<br></blockquote><blockquote type="cite">; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0<br></blockquote><blockquote type="cite">;<br></blockquote><blockquote type="cite">; for use with GROMACS 3.3<br></blockquote><blockquote type="cite">;<br></blockquote><blockquote type="cite">; VARIOUS PREPROCESSING OPTIONS =<br></blockquote><blockquote type="cite">title = Martini<br></blockquote><blockquote type="cite">cpp = /usr/bin/cpp<br></blockquote><blockquote type="cite">define = -DPOSREBB<br></blockquote><blockquote type="cite">; RUN CONTROL PARAMETERS =<br></blockquote><blockquote type="cite">; MARTINI - Most simulations are stable with dt=40 fs,<br></blockquote><blockquote type="cite">; some (especially rings) require 20-30 fs.<br></blockquote><blockquote type="cite">; The range of time steps used for parametrization<br></blockquote><blockquote type="cite">; is 20-40 fs, using smaller time steps is therefore not recommended.<br></blockquote><blockquote type="cite">integrator = md<br></blockquote><blockquote type="cite">; start time and timestep in ps<br></blockquote><blockquote type="cite">tinit = 0.0<br></blockquote><blockquote type="cite">dt = 0.030<br></blockquote><blockquote type="cite">nsteps = 1000000<br></blockquote><blockquote type="cite">; number of steps for center of mass motion removal =<br></blockquote><blockquote type="cite">nstcomm = 1<br></blockquote><blockquote type="cite">comm-mode = Linear<br></blockquote><blockquote type="cite">comm-grps = Protein_Lipids W<br></blockquote><blockquote type="cite">; OUTPUT CONTROL OPTIONS =<br></blockquote><blockquote type="cite">; Output frequency for coords (x), velocities (v) and forces (f) =<br></blockquote><blockquote type="cite">nstxout = 5000<br></blockquote><blockquote type="cite">nstvout = 5000<br></blockquote><blockquote type="cite">nstfout = 0<br></blockquote><blockquote type="cite">; Output frequency for energies to log file and energy file =<br></blockquote><blockquote type="cite">nstlog = 1000<br></blockquote><blockquote type="cite">nstenergy = 1000<br></blockquote><blockquote type="cite">; Output frequency and precision for xtc file =<br></blockquote><blockquote type="cite">nstxtcout = 1000<br></blockquote><blockquote type="cite">xtc_precision = 100<br></blockquote><blockquote type="cite">; This selects the subset of atoms for the xtc file. You can =<br></blockquote><blockquote type="cite">; select multiple groups. By default all atoms will be written. =<br></blockquote><blockquote type="cite">xtc-grps =<br></blockquote><blockquote type="cite">; Selection of energy groups =<br></blockquote><blockquote type="cite">energygrps =<br></blockquote><blockquote type="cite">; NEIGHBORSEARCHING PARAMETERS =<br></blockquote><blockquote type="cite">; MARTINI - no need for more frequent updates<br></blockquote><blockquote type="cite">; or larger neighborlist cut-off due<br></blockquote><blockquote type="cite">; to the use of shifted potential energy functions.<br></blockquote><blockquote type="cite">; nblist update frequency =<br></blockquote><blockquote type="cite">nstlist = 10<br></blockquote><blockquote type="cite">; ns algorithm (simple or grid) =<br></blockquote><blockquote type="cite">ns_type = grid<br></blockquote><blockquote type="cite">; Periodic boundary conditions: xyz or none =<br></blockquote><blockquote type="cite">pbc = xyz<br></blockquote><blockquote type="cite">; nblist cut-off =<br></blockquote><blockquote type="cite">rlist = 1.2<br></blockquote><blockquote type="cite">; OPTIONS FOR ELECTROSTATICS AND VDW =<br></blockquote><blockquote type="cite">; MARTINI - vdw and electrostatic interactions are used<br></blockquote><blockquote type="cite">; in their shifted forms. Changing to other types of<br></blockquote><blockquote type="cite">; electrostatics will affect the general performance of<br></blockquote><blockquote type="cite">; the model.<br></blockquote><blockquote type="cite">; Method for doing electrostatics =<br></blockquote><blockquote type="cite">coulombtype = Shift<br></blockquote><blockquote type="cite">rcoulomb_switch = 0.0<br></blockquote><blockquote type="cite">rcoulomb = 1.2<br></blockquote><blockquote type="cite">; Dielectric constant (DC) for cut-off or DC of reaction field =<br></blockquote><blockquote type="cite">epsilon_r = 15<br></blockquote><blockquote type="cite">; Method for doing Van der Waals =<br></blockquote><blockquote type="cite">vdw_type = Shift<br></blockquote><blockquote type="cite">; cut-off lengths =<br></blockquote><blockquote type="cite">rvdw_switch = 0.9<br></blockquote><blockquote type="cite">rvdw = 1.2<br></blockquote><blockquote type="cite">; Apply long range dispersion corrections for Energy and Pressure =<br></blockquote><blockquote type="cite">DispCorr = No<br></blockquote><blockquote type="cite">; OPTIONS FOR WEAK COUPLING ALGORITHMS =<br></blockquote><blockquote type="cite">; MARTINI - normal temperature and pressure coupling schemes<br></blockquote><blockquote type="cite">; can be used. It is recommended to couple individual groups<br></blockquote><blockquote type="cite">; in your system seperately.<br></blockquote><blockquote type="cite">; Temperature coupling =<br></blockquote><blockquote type="cite">tcoupl = Nose-Hoover<br></blockquote><blockquote type="cite">nsttcouple = 1<br></blockquote><blockquote type="cite">; Groups to couple separately =<br></blockquote><blockquote type="cite">tc-grps = Protein W Lipids<br></blockquote><blockquote type="cite">; Time constant (ps) and reference temperature (K) =<br></blockquote><blockquote type="cite">tau_t = 1.2 1.2 1.2<br></blockquote><blockquote type="cite">ref_t = 296 296 296<br></blockquote><blockquote type="cite">; Pressure coupling =<br></blockquote><blockquote type="cite">Pcoupl = Parrinello-Rahman<br></blockquote><blockquote type="cite">Pcoupltype = semiisotropic<br></blockquote><blockquote type="cite">nstpcouple = 1<br></blockquote><blockquote type="cite">; Time constant (ps), compressibility (1/bar) and reference P (bar) =<br></blockquote><blockquote type="cite">tau_p = 12.0<br></blockquote><blockquote type="cite">compressibility = 3e-5 3e-5<br></blockquote><blockquote type="cite">ref_p = 1.0 1.0<br></blockquote><blockquote type="cite">; GENERATE VELOCITIES FOR STARTUP RUN =<br></blockquote><blockquote type="cite">gen_vel = no<br></blockquote><blockquote type="cite">gen_temp = 296<br></blockquote><blockquote type="cite">gen_seed = 666<br></blockquote><blockquote type="cite">; Distance restraints type: No, Simple or Ensemble<br></blockquote><blockquote type="cite">disre = Simple<br></blockquote><blockquote type="cite">; Force weighting of pairs in one distance restraint: Conservative or Equal<br></blockquote><blockquote type="cite">disre-weighting = Conservative<br></blockquote><blockquote type="cite">; Use sqrt of the time averaged times the instantaneous violation<br></blockquote><blockquote type="cite">disre-mixed = no<br></blockquote><blockquote type="cite">disre-fc = 500<br></blockquote><blockquote type="cite">disre-tau = 0<br></blockquote><blockquote type="cite">; Output frequency for pair distances to energy file<br></blockquote><blockquote type="cite">nstdisreout = 100<br></blockquote><blockquote type="cite">; OPTIONS FOR BONDS =<br></blockquote><blockquote type="cite">; MARTINI - for ring systems constraints are defined<br></blockquote><blockquote type="cite">; which are best handled using Lincs.<br></blockquote><blockquote type="cite">constraints = none<br></blockquote><blockquote type="cite">; Type of constraint algorithm =<br></blockquote><blockquote type="cite">constraint_algorithm = Lincs<br></blockquote><blockquote type="cite">; Do not constrain the start configuration =<br></blockquote><blockquote type="cite">unconstrained_start = yes<br></blockquote><blockquote type="cite">; Highest order in the expansion of the constraint coupling matrix =<br></blockquote><blockquote type="cite">lincs_order = 4<br></blockquote><blockquote type="cite">; Lincs will write a warning to the stderr if in one step a bond =<br></blockquote><blockquote type="cite">; rotates over more degrees than =<br></blockquote><blockquote type="cite">lincs_warnangle = 30<br></blockquote><blockquote type="cite">; FREEZE GROUPS<br></blockquote><blockquote type="cite">freezegrps =<br></blockquote><blockquote type="cite">freezedim =<br></blockquote><blockquote type="cite">; CONTINUATION<br></blockquote><blockquote type="cite">; this is specified by using -t -e flags in grompp and unconstrained_start = yes<br></blockquote><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- <br>gmx-users mailing list gmx-users@gromacs.org<br>http://lists.gromacs.org/mailman/listinfo/gmx-users<br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br></div></blockquote></div><br></div></body></html>