Re: [gmx-users] Re: solution molecules cannot be set by mdrun after neutralization
Stefano Meliga wrote: Hi again, The energy minimization with conjugate gradient integrator still gives me two warnings of the type: t = 0.011 ps: Water molecule starting at atom 28122 can not be settled. Check for bad contacts and/or reduce the timestep. OK I checked the code, and reporting a timestep is erroneous. Apologies for my misleading advice earlier. I filed a bugzilla about the message. It likely should read "Step 11: Water molecule..." Nonetheless, the water at around 28122 may have had a serious problem that is worth checking out, lest something break later on in the simulation. Mark My command lines are: $grxdir/grompp -f 4AKEpreEMcg.mdp -po 4AKE_EMcg.mdp -c 4AKE_EMsteep.gro -p 4AKEallHion.top -pp 4AKEpreEMsteep.top -o 4AKE_EMcg.tpr $grxdir/mdrun -s 4AKE_EMcg.tpr -o 4AKE_EMcg.trr -c 4AKE_EMcg.gro -e 4AKE_EMcg.edr -g 4AKE_EMcg.log -v This is my mdp file 4AKEpreEMcg.mdp: title = 4AKE_EMcg cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = cg nsteps = 1500 nstlist = 50 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; ; Energy minimizing stuff ; emtol = 1.0 emstep = 0.01 The minimization is successful but I don't see the meaning of this timestep. Thanks, Stefano. Justin A. Lemkul ha scritto: Stefano Meliga wrote: My integrator is "steep", which should perform EM. This is my mdp file: title = 4AKE_PREMsteep cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = all-bonds integrator = steep nsteps = 500 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 DispCorr = no ; ; Energy minimizing stuff ; emtol = 1.0 emstep = 0.01 I learnt from the tutorials (s-peptide) that in order to do a position restrained MD the I have to set the constraints (all-bonds in this case). Is that incorrect? Is it valid for EM as well? Position restraints != bond contraints. Using "constraints = all-bonds" will constrain the bond lengths, but not restrain the positions of the atoms. If you want to do position-restrained MD, you have to "define = -DPOSRES" (according to the #ifdef POSRES block in the topology, assuming you made one automatically from pdb2gmx). Using position restraints in EM doesn't serve much of a purpose in my mind, unless you really need to preserve the exact initial configuration; it may in fact prevent your system from converging if some bad geometry is being held in place. -Justin Thank you for your advice, Stefano. Mark Abraham ha scritto: Stefano Meliga wrote: Hi again, I've tryed to perform the same preprocessing and EM steps without distance constraints and the situation improves a lot. I get no warnings in the steepest descent EM and only one molecule cannot be set in the conjugate gradient EM. Can you see the reason? Yes. You're not doing EM. "t = 0.011 ps:" is a big clue. Choose your integrator in your .mdp file better. Also, as Justin suggests, please be careful with the constraint/restraint terminology. Mark Thanks, Stefano. Stefano Meliga ha scritto: 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 mol
Re: [gmx-users] Re: solution molecules cannot be set by mdrun after neutralization
On Jun 1, 2009, at 1:12 PM, Stefano Meliga wrote: Hi again, The energy minimization with conjugate gradient integrator still gives me two warnings of the type: t = 0.011 ps: Water molecule starting at atom 28122 can not be settled. Check for bad contacts and/or reduce the timestep. My command lines are: $grxdir/grompp -f 4AKEpreEMcg.mdp -po 4AKE_EMcg.mdp -c 4AKE_EMsteep.gro -p 4AKEallHion.top -pp 4AKEpreEMsteep.top -o 4AKE_EMcg.tpr $grxdir/mdrun -s 4AKE_EMcg.tpr -o 4AKE_EMcg.trr -c 4AKE_EMcg.gro -e 4AKE_EMcg.edr -g 4AKE_EMcg.log -v This is my mdp file 4AKEpreEMcg.mdp: title = 4AKE_EMcg cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = cg nsteps = 1500 nstlist = 50 change that to 1 if it does not get better it means that your system is build in such a way that you have bad contacts that the minimization can not remove. You have to check where there are and do something about it. ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; ; Energy minimizing stuff ; emtol = 1.0 emstep = 0.01 The minimization is successful but I don't see the meaning of this timestep. Thanks, Stefano. Justin A. Lemkul ha scritto: Stefano Meliga wrote: My integrator is "steep", which should perform EM. This is my mdp file: title = 4AKE_PREMsteep cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = all-bonds integrator = steep nsteps = 500 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 DispCorr = no ; ; Energy minimizing stuff ; emtol = 1.0 emstep = 0.01 I learnt from the tutorials (s-peptide) that in order to do a position restrained MD the I have to set the constraints (all- bonds in this case). Is that incorrect? Is it valid for EM as well? Position restraints != bond contraints. Using "constraints = all- bonds" will constrain the bond lengths, but not restrain the positions of the atoms. If you want to do position-restrained MD, you have to "define = - DPOSRES" (according to the #ifdef POSRES block in the topology, assuming you made one automatically from pdb2gmx). Using position restraints in EM doesn't serve much of a purpose in my mind, unless you really need to preserve the exact initial configuration; it may in fact prevent your system from converging if some bad geometry is being held in place. -Justin Thank you for your advice, Stefano. Mark Abraham ha scritto: Stefano Meliga wrote: Hi again, I've tryed to perform the same preprocessing and EM steps without distance constraints and the situation improves a lot. I get no warnings in the steepest descent EM and only one molecule cannot be set in the conjugate gradient EM. Can you see the reason? Yes. You're not doing EM. "t = 0.011 ps:" is a big clue. Choose your integrator in your .mdp file better. Also, as Justin suggests, please be careful with the constraint/ restraint terminology. Mark Thanks, Stefano. Stefano Meliga ha scritto: 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 io
Re: [gmx-users] Re: solution molecules cannot be set by mdrun after neutralization
Hi again, The energy minimization with conjugate gradient integrator still gives me two warnings of the type: t = 0.011 ps: Water molecule starting at atom 28122 can not be settled. Check for bad contacts and/or reduce the timestep. My command lines are: $grxdir/grompp -f 4AKEpreEMcg.mdp -po 4AKE_EMcg.mdp -c 4AKE_EMsteep.gro -p 4AKEallHion.top -pp 4AKEpreEMsteep.top -o 4AKE_EMcg.tpr $grxdir/mdrun -s 4AKE_EMcg.tpr -o 4AKE_EMcg.trr -c 4AKE_EMcg.gro -e 4AKE_EMcg.edr -g 4AKE_EMcg.log -v This is my mdp file 4AKEpreEMcg.mdp: title = 4AKE_EMcg cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = cg nsteps = 1500 nstlist = 50 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; ; Energy minimizing stuff ; emtol = 1.0 emstep = 0.01 The minimization is successful but I don't see the meaning of this timestep. Thanks, Stefano. Justin A. Lemkul ha scritto: Stefano Meliga wrote: My integrator is "steep", which should perform EM. This is my mdp file: title = 4AKE_PREMsteep cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = all-bonds integrator = steep nsteps = 500 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 DispCorr = no ; ; Energy minimizing stuff ; emtol = 1.0 emstep = 0.01 I learnt from the tutorials (s-peptide) that in order to do a position restrained MD the I have to set the constraints (all-bonds in this case). Is that incorrect? Is it valid for EM as well? Position restraints != bond contraints. Using "constraints = all-bonds" will constrain the bond lengths, but not restrain the positions of the atoms. If you want to do position-restrained MD, you have to "define = -DPOSRES" (according to the #ifdef POSRES block in the topology, assuming you made one automatically from pdb2gmx). Using position restraints in EM doesn't serve much of a purpose in my mind, unless you really need to preserve the exact initial configuration; it may in fact prevent your system from converging if some bad geometry is being held in place. -Justin Thank you for your advice, Stefano. Mark Abraham ha scritto: Stefano Meliga wrote: Hi again, I've tryed to perform the same preprocessing and EM steps without distance constraints and the situation improves a lot. I get no warnings in the steepest descent EM and only one molecule cannot be set in the conjugate gradient EM. Can you see the reason? Yes. You're not doing EM. "t = 0.011 ps:" is a big clue. Choose your integrator in your .mdp file better. Also, as Justin suggests, please be careful with the constraint/restraint terminology. Mark Thanks, Stefano. Stefano Meliga ha scritto: 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 listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http:
Re: [gmx-users] Re: solution molecules cannot be set by mdrun after neutralization
Stefano Meliga wrote: My integrator is "steep", which should perform EM. This is my mdp file: title = 4AKE_PREMsteep cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = all-bonds integrator = steep nsteps = 500 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 DispCorr = no ; ; Energy minimizing stuff ; emtol = 1.0 emstep = 0.01 I learnt from the tutorials (s-peptide) that in order to do a position restrained MD the I have to set the constraints (all-bonds in this case). Is that incorrect? Is it valid for EM as well? Position restraints != bond contraints. Using "constraints = all-bonds" will constrain the bond lengths, but not restrain the positions of the atoms. If you want to do position-restrained MD, you have to "define = -DPOSRES" (according to the #ifdef POSRES block in the topology, assuming you made one automatically from pdb2gmx). Using position restraints in EM doesn't serve much of a purpose in my mind, unless you really need to preserve the exact initial configuration; it may in fact prevent your system from converging if some bad geometry is being held in place. -Justin Thank you for your advice, Stefano. Mark Abraham ha scritto: Stefano Meliga wrote: Hi again, I've tryed to perform the same preprocessing and EM steps without distance constraints and the situation improves a lot. I get no warnings in the steepest descent EM and only one molecule cannot be set in the conjugate gradient EM. Can you see the reason? Yes. You're not doing EM. "t = 0.011 ps:" is a big clue. Choose your integrator in your .mdp file better. Also, as Justin suggests, please be careful with the constraint/restraint terminology. Mark Thanks, Stefano. Stefano Meliga ha scritto: 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 listgmx-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 ___ gmx-users mailing listgmx-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 ___ gmx-users mailing listgmx-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 -- =
Re: [gmx-users] Re: solution molecules cannot be set by mdrun after neutralization
My integrator is "steep", which should perform EM. This is my mdp file: title = 4AKE_PREMsteep cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = all-bonds integrator = steep nsteps = 500 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 DispCorr = no ; ; Energy minimizing stuff ; emtol = 1.0 emstep = 0.01 I learnt from the tutorials (s-peptide) that in order to do a position restrained MD the I have to set the constraints (all-bonds in this case). Is that incorrect? Is it valid for EM as well? Thank you for your advice, Stefano. Mark Abraham ha scritto: Stefano Meliga wrote: Hi again, I've tryed to perform the same preprocessing and EM steps without distance constraints and the situation improves a lot. I get no warnings in the steepest descent EM and only one molecule cannot be set in the conjugate gradient EM. Can you see the reason? Yes. You're not doing EM. "t = 0.011 ps:" is a big clue. Choose your integrator in your .mdp file better. Also, as Justin suggests, please be careful with the constraint/restraint terminology. Mark Thanks, Stefano. Stefano Meliga ha scritto: 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 listgmx-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 ___ gmx-users mailing listgmx-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 ___ gmx-users mailing listgmx-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
Re: [gmx-users] Re: solution molecules cannot be set by mdrun after neutralization
Stefano Meliga wrote: Hi again, I've tryed to perform the same preprocessing and EM steps without distance constraints and the situation improves a lot. I get no warnings in the steepest descent EM and only one molecule cannot be set in the conjugate gradient EM. Can you see the reason? Yes. You're not doing EM. "t = 0.011 ps:" is a big clue. Choose your integrator in your .mdp file better. Also, as Justin suggests, please be careful with the constraint/restraint terminology. Mark Thanks, Stefano. Stefano Meliga ha scritto: 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 listgmx-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 ___ gmx-users mailing listgmx-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
Re: [gmx-users] Re: solution molecules cannot be set by mdrun after neutralization
Stefano Meliga wrote: Hi again, I've tryed to perform the same preprocessing and EM steps without distance constraints and the situation improves a lot. I get no warnings in the steepest descent EM and only one molecule cannot be set in the conjugate gradient EM. Can you see the reason? Were you constraining bond lengths or using position restraints? You've combined the terminology (restraints and constraints are separate ideas in Gromacs). LINCS warnings and related problems are discussed extensively in the list archive (with potential solutions!) as well as on the wiki: http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings If the problem arises only after adding ions, inspect the location of ion insertion. Since it is random, ions may have been placed in an unfavorable location, causing them (or a nearby water molecule) to go careening through the simulation cell. That happened to me once :) -Justin Thanks, Stefano. Stefano Meliga ha scritto: 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 listgmx-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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-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
[gmx-users] Re: solution molecules cannot be set by mdrun after neutralization
Hi again, I've tryed to perform the same preprocessing and EM steps without distance constraints and the situation improves a lot. I get no warnings in the steepest descent EM and only one molecule cannot be set in the conjugate gradient EM. Can you see the reason? Thanks, Stefano. Stefano Meliga ha scritto: 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 listgmx-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
