Hi everybody, I neutralized my system with the commands:
$grxdir/grompp -f dummy.mdp -po dummyout.mdp -c 4AKEallHsol.gro -p 4AKEallH.top -pp 4AKEallHsol_pre.top -o 4AKEallHsol.tpr $grxdir/genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p 4AKEallHsol_pre.top -np 4 -pname NA+ -g -pot 4AKEallHion.pdb -nname CL- (adding the atoms to the solution SOL) I renamed the files to keep track of the different topology files: mv 4AKEallHsol_pre.top 4AKEallHion.top mv "#4AKEallHsol_pre.top.1#" 4AKEallHsol_pre.top I run an all-bonds position restraint steepest descent EM: $grxdir/grompp -f 4AKEprePREMsteep.mdp -po 4AKE_PREMsteep.mdp -c 4AKEallHion.gro -p 4AKEallHion.top -pp 4AKEallHion_out.top -o 4AKEallHion.tpr $grxdir/mdrun -s 4AKEallHion.tpr -o 4AKE_PREMsteep.trr -c 4AKE_PREMsteep.gro -e 4AKE_PREMsteep.edr -g 4AKE_PREMsteep.log -v mdrun exits successfully but displays the warning: t = 0.011 ps: Water molecule starting at atom 17223 can not be settled. Check for bad contacts and/or reduce the timestep. In the gro file atom 17223 is an oxigen of the solution Going further with my simulation i run a all-bonds position restrained conjugate gradient EM: $grxdir/grompp -f 4AKEprePREMcg.mdp -po 4AKE_PREMcg.mdp -c 4AKE_PREMsteep.gro -p 4AKEallHion_out.top -pp 4AKEallH_PREMsteep.top -o 4AKEallH_PREMsteep.tpr $grxdir/mdrun -s 4AKEallH_PREMsteep.tpr -o 4AKE_PREMcg.trr -c 4AKE_PREMcg.gro -e 4AKE_PREMcg.edr -g 4AKE_PREMcg.log -v but get the fatal error: Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (2200) And some of this warnings are again solution's molecules that cannot be set. May the problem be related to the ions added to neutralise the system? mdrun was not showing this problem with the non-neutral system in input. Thanks a lot, Stefano _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
