I used the mdp file listed previously to generate the tpr file. It gave this warning:
WARNING 1 [file membed.mdp]: Can not exclude the lattice Coulomb energy between energy groups then I ignored the warning with -maxwarn 1 and gave the tpr file to g_membed, command line like this: g_membed -f membed.tpr -p topol.top -xyinit 0.1 -xyend 1.0 -nxy 1000 Then it seems the g_membed did one iteration and stopped , it returned this: Back Off! I just backed up step1b.pdb to ./#step1b.pdb.2# Back Off! I just backed up step1c.pdb to ./#step1c.pdb.2# Wrote pdb files with previous and current coordinates ------------------------------------------------------- Program g_membed, VERSION 4.5.3 Source code file: nsgrid.c, line: 540 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- I am wondering if it is because the parameters in the mdp file set improper. How to change it? Linda Does this mean that I need to 2011/11/11 Mark Abraham <mark.abra...@anu.edu.au>: > On 11/11/2011 5:13 PM, LindaSong wrote: > > Thank you very much for your reply, Mark > > It is the topology problem. It seems I did it in a wrong way. Now the > topology goes like this: > [ molecules ] > ; Compound #mols > Protein_chain_A 1 > Protein_chain_A2 1 > POPC 256 > This problem solved. > > But then comes a new one. When I did the g_membed, the system blowed up > after one iteration! > I think I really shouldn't ignore the warning from the grompp. However, as > an inexper ienced user, I don't know how to improve the mdp file. Can you > give me any hint? > > Use a text editor that writes plain text. Junk " " throughout cannot > help things. As before, reporting the actual text of the warning is critical > to working out what might be wrong. > > Mark > > The mdp file for the g_membed is like this: > > cpp = /lib/cpp > ; Run parameters > integrator = md > nsteps = 1000 > dt = 0.002 > ; Output control > nstxout = 10&n bsp; > nstvout = 10 > nstenergy = 10 > nstlog = 10 > ; Bond parameters > continuation = no > constraint_algorithm = lincs > constraints = all-bonds > lincs_iter = 1 > lincs_order = 4 > ; Neighborsearching > ns_type = grid > nstlist = 1 > rlist = 1.4 > rcoulomb = 1.4 > rvdw &nb sp; = 1.4 > ; Electrostatics > coulombtype = PME > pme_order = 4 > fourierspacing = 0.16 > ; Temperature coupling is on > tcoupl = V-rescale > tc-grps = Protein Non-Protein > tau_t = 0.1 0.1 & nbsp; > ref_t = 300 300 > ; Pressure coupling is on > Pcoupl = Berendsen > pcoupltype = semiisotropic > tau_p = 1.0 > compressibility = 4.5e-5 4.5e-5 > ref_p ; = 1.0 1.0 > ; Velocity generation > gen_vel = yes > gen_temp = 300 > gen_seed = 173529 > ; Energy monitoring > energygrps = Protein > ; Non-equilibrium MD > freezegrps = Protein > freezedim &nb sp; = Y Y Y > ; Energy group exclusions > energygrp_excl = Protein Protein > > Thanks a lot! > Linda > > > > > > > > > > -- > 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 > -- 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
