Hi Gmxusers,
I have been trying to run mdrun -rerun to get the energy of the protein in my protein-lipid system. I know similar questions have been raised on this topic before, I have tried to glean useful information from them to solve my problem but unfortunately to no avail. Thanks for your patience! As I did not have energygrps in the initial .mdp file, I included it this time integrator = md nsteps = 0 dt = 0.002 nstxout = 50000 nstvout = 50000 nstenergy = 500 nstlog = 500 Continuation = yes constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ns_type = grid nstlist = 5 rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 coulombtype = PME pme_order = 4 fourierspacing = 0.16 tcoupl = Nose-Hoover tc-grps = Protein POPE SOL_CL- tau_t = 0.1 0.1 0.1 ref_t = 323 323 323 pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 ref_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 pbc = xyz DispCorr = EnerPres gen_vel = no nstcomm = 1 comm-mode = Linear comm-grps = Protein_POPE SOL_CL- energygrps = Protein SOL POPE I then did 1)grompp -f new.mdp -n index.ndx -c old.tpr -o rerun.tpr -p topol.top 2)trjconv -f old.trr -n index.ndx -s rerun.tpr -o rerun.trr (when prompted, I selected "0" system) 3)mdrun -s rerun.tpr -rerun rerun.trr I notice that the previous post http://oldwww.gromacs.org/pipermail/gmx-users/2009-January/038968.html suggested to use tpbconv (on rerun.tpr) and trjconv (on rerun.trr) to extract the protein only. While it was possible to do so with trjconv, it wasn't feasible with tpbconv (I'm using gromacs 4.0.7) - I might have missed out something as I did not get any prompt/output (see below) tpbconv -s topol.tpr -n index_P.ndx -o rerun2.tpr Reading toplogy and shit from topol.tpr Reading file topol.tpr, VERSION 4.0.7 (single precision) 0 steps (0 ps) remaining from first run. You've simulated long enough. Not writing tpr file Using the g_energy command on the output energy.edr file, I got among others, these options to choose 49 Coul-SR:Protein-Protein 50 LJ-SR:Protein-Protein 51 Coul-14:Protein-Protein 52 LJ-14:Protein-Protein In order to get the energy of the protein, I reckon I have to add 49,50,51,52 (to account for the nonbonded components) and 1 Angle 2 G96Angle 3 Proper-Dih. 4 Ryckaert-Bell. 5 Improper-Dih for the bonded components. However, I think 1-5 is the bonded terms for the system and not the protein alone. Can anyone help me with this? Also, on a slightly different note, this post http://oldwww.gromacs.org/pipermail/gmx-users/2005-July/016307.html suggested that the force constant of the solvent (DMSO) to be adjusted to zero. Am I right to think that it does not apply to my case as my protein-lipid system is solvated with SPC? (I read that SPC is rigid water. I did not add -DFLEXIBLE in .mdp) Any help would be highly appreciated.Thanks! HW << This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK & Malaysia legislation. >>
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