Hi Justin, Thanks for the suggestion I got it solved somehow. The main problem was in the popc128b.pdb itself, it has first 64 lipids and half of the SOl molecules followed by rest of the POPC and SOL molecules. When I rearranged them the error was solved.
But now another thing I would like to confirm with you. During shrinking stage, I get the following notes, please tell me are they OK at this stage, NOTE 1 [file topol.top, line 3070]: System has non-zero total charge: 5.000000e+00 Analysing residue names: There are: 46 Protein residues There are: 126 Other residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 21063.00 Largest charge group radii for Van der Waals: 0.249, 0.247 nm Largest charge group radii for Coulomb: 0.249, 0.247 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 160x160x48, spacing 0.110 0.114 0.119 Estimate for the relative computational load of the PME mesh part: 0.92 NOTE 2 [file em_st.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing This run will generate roughly 17 Mb of data There were 2 notes Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999391.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
