Dear Justin Thanks for your reply
> You're still working with outdated software. Please follow my > suggestion of trying 4.6.3. I try to install 4.6.3. > The larger issue, in the end, is the unphysical configuration of the drug > in the membrane. Independent of Gromacs version, that setup will > always fail. I did minimization in 2 other states: 1) without drug (only membrane: DOPC nad cholesterol). 2) with drug but, this time, I put drug into water molecules not into membrane. Then I did mdrun for both of states. In both of state, there are not following issues: Warning: 1-4 interaction between 434 and 407 at distance 3.023 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size step 23: Water molecule starting at atom 10613 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates -------------------------------------------------------------------------- There are following outputs: for state 1) ------------- Reading file em.tpr, VERSION 4.5.1 (single precision) Starting 4 threads Making 2D domain decomposition 1 x 2 x 2 Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 881 steps, but did not reach the requested Fmax < 1000. Potential Energy = 2.1828770e+05 Maximum force = 1.3656898e+04 on atom 618 Norm of force = 5.1748779e+02 -------------------------------------------------------------------- for state 2) ---------------- Reading file em.tpr, VERSION 4.5.1 (single precision) Starting 4 threads Making 2D domain decomposition 1 x 2 x 2 Back Off! I just backed up em.trr to ./#em.trr.1# Back Off! I just backed up em.edr to ./#em.edr.1# Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.1# Steepest Descents converged to machine precision in 845 steps, but did not reach the requested Fmax < 1000. Potential Energy = 1.9664772e+05 Maximum force = 1.0986521e+04 on atom 241 Norm of force = 4.4174323e+02 --------------------------------------------------------------------------- When I see created gro file from minimization (em.gro), I see some dopc and cholesterol molecules were broken and they devided 2 or 3 parts. Input gro file (system.gro) has 1835 residues. Created gro file from minimization (em.gro) has 1835 residues. But when I load em.gro file in VMD, there are 1950 residues in graphical representation --> selections --> residues part. Can I deduce my problem has not dependent to presence of drug? Are there problem about my force field parameters or topology file ? I get force field parameters from lipid book (for dopc and cholesterol) and from prodrg server (for drug). Please help me to resolve this issue. Best wishes for you -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
