Re: [gmx-users] Strange problem with simple FEP (bug?)
Thanks, but that's indeed not the problem. I'm just doing a PR-run in state A. State B is not of interest in that case. Somehow GROMACS mixes things up internally, I guess. The bugzilla-entry has been placed. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ David Mobley wrote: Maik, I'm trying to do a simple FEP within a simple protein, which seems to make things simple...but as you may expect...it is anything else than that. What I'm trying to do is morphing a Tyrosine into a Phenylalanine in OPLSAA. Therefore the CZ is changed from the type of TYR to the type of PHE. The oxygen(TYR) is changed to a proton(PHE) and the proton(TYR) to a dummy (PHE). So this is very simple. We checked the tpr-dump and everything looks fine (except, maybe, we missed it). Now, in the position-restraint run (where state B should not be regarded by the system), the OH-proton moves on top of the OH-oxygen and the simulation crashes after a while. We then performed a FEP from TYR to TYR (so A- and B-state are the same) and the system runs. I am not an OPLS guy myself, and I don't know the details of your transformation, so I'll just tell you one possibility, and you'll have to decide whether it could apply in your situation. Sometimes, if you are disappearing a Lennard-Jones site that still has some amount of electrostatics, it can begin to interpenetrate with other atoms which either do not have Lennard-Jones interactions (hydrogens in some force fields) or which do (depending on the combination rule you use). Obviously, this is bad because (for example) protons can move on top of oxygens and cause blowing up. A classic example of this is, for example, if I am turning off the LJ on an oxygen site at the same time as turning off the charges on that oxygen. In many FF's, water hydrogens lack LJ interactions, so they can come and overlap with the oxygen I'm disappearing, which is still charged (at least to some degree) and cause a "fusion" type event. I don't know if that's what's going on for you, but you might think about it -- do you have any atoms that you're disappearing, and are there other atoms which the combination rules would allow to overlap with those? The way I get around this problem in my calculations is to always turn off electrostatics on any atom I'm disappearing prior to modifying the LJ parameters, so that I never have a charged atom which is being treated using the "soft-core" potentials that allow overlap. Not sure if that's your problem -- just a thought. David The whole thing was done with GROMACS 3.3.1 and TIP4P. Any suggestions? Gerrit and me think of a bug somewhere. Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] 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 don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] 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 don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Strange problem with simple FEP (bug?)
Maik, I'm trying to do a simple FEP within a simple protein, which seems to make things simple...but as you may expect...it is anything else than that. What I'm trying to do is morphing a Tyrosine into a Phenylalanine in OPLSAA. Therefore the CZ is changed from the type of TYR to the type of PHE. The oxygen(TYR) is changed to a proton(PHE) and the proton(TYR) to a dummy (PHE). So this is very simple. We checked the tpr-dump and everything looks fine (except, maybe, we missed it). Now, in the position-restraint run (where state B should not be regarded by the system), the OH-proton moves on top of the OH-oxygen and the simulation crashes after a while. We then performed a FEP from TYR to TYR (so A- and B-state are the same) and the system runs. I am not an OPLS guy myself, and I don't know the details of your transformation, so I'll just tell you one possibility, and you'll have to decide whether it could apply in your situation. Sometimes, if you are disappearing a Lennard-Jones site that still has some amount of electrostatics, it can begin to interpenetrate with other atoms which either do not have Lennard-Jones interactions (hydrogens in some force fields) or which do (depending on the combination rule you use). Obviously, this is bad because (for example) protons can move on top of oxygens and cause blowing up. A classic example of this is, for example, if I am turning off the LJ on an oxygen site at the same time as turning off the charges on that oxygen. In many FF's, water hydrogens lack LJ interactions, so they can come and overlap with the oxygen I'm disappearing, which is still charged (at least to some degree) and cause a "fusion" type event. I don't know if that's what's going on for you, but you might think about it -- do you have any atoms that you're disappearing, and are there other atoms which the combination rules would allow to overlap with those? The way I get around this problem in my calculations is to always turn off electrostatics on any atom I'm disappearing prior to modifying the LJ parameters, so that I never have a charged atom which is being treated using the "soft-core" potentials that allow overlap. Not sure if that's your problem -- just a thought. David The whole thing was done with GROMACS 3.3.1 and TIP4P. Any suggestions? Gerrit and me think of a bug somewhere. Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] 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 don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Strange problem with simple FEP (bug?)
Maik Goette wrote: Update: Checked it with the Amber99 port. Same strange habit. It occured with another protein (system), too. please submit a bugzilla. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Strange problem with simple FEP (bug?)
Update: Checked it with the Amber99 port. Same strange habit. It occured with another protein (system), too. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Maik Goette wrote: Hey all I'm trying to do a simple FEP within a simple protein, which seems to make things simple...but as you may expect...it is anything else than that. What I'm trying to do is morphing a Tyrosine into a Phenylalanine in OPLSAA. Therefore the CZ is changed from the type of TYR to the type of PHE. The oxygen(TYR) is changed to a proton(PHE) and the proton(TYR) to a dummy (PHE). So this is very simple. We checked the tpr-dump and everything looks fine (except, maybe, we missed it). Now, in the position-restraint run (where state B should not be regarded by the system), the OH-proton moves on top of the OH-oxygen and the simulation crashes after a while. We then performed a FEP from TYR to TYR (so A- and B-state are the same) and the system runs. The whole thing was done with GROMACS 3.3.1 and TIP4P. Any suggestions? Gerrit and me think of a bug somewhere. Regards ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Strange problem with simple FEP (bug?)
Hey all I'm trying to do a simple FEP within a simple protein, which seems to make things simple...but as you may expect...it is anything else than that. What I'm trying to do is morphing a Tyrosine into a Phenylalanine in OPLSAA. Therefore the CZ is changed from the type of TYR to the type of PHE. The oxygen(TYR) is changed to a proton(PHE) and the proton(TYR) to a dummy (PHE). So this is very simple. We checked the tpr-dump and everything looks fine (except, maybe, we missed it). Now, in the position-restraint run (where state B should not be regarded by the system), the OH-proton moves on top of the OH-oxygen and the simulation crashes after a while. We then performed a FEP from TYR to TYR (so A- and B-state are the same) and the system runs. The whole thing was done with GROMACS 3.3.1 and TIP4P. Any suggestions? Gerrit and me think of a bug somewhere. Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
