RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other way to do this? Otherwise I have to manually translate the system back to its original position in the box after the simulation has crashed and then continue the simulation, but this is not very good since I cannot use the checkpoint file then and the continuation is not exact. Any suggestion what to do? Thanks in advance. Emma Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] Skickat: den 27 april 2010 16:32 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box you should remove the water and lipid bilayer COM separately. I am not sure what you should do with your small molecule though. Probably best to add it to the bilayer as you constrain their relative position! On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Sorry that I didn't understand you explanation. Emma Från: gmx-users-boun...@gromacs.orgmailto:gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.orgmailto:gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nlmailto:x.peri...@rug.nl] Skickat: den 27 april 2010 12:41 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= membrane solvent+ions On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: Hi all! I have a problem regarding lipid bilayer simulations in Gromacs 4. During some of my simulations the whole system is moving in the z direction in the box, meaning that after some time the lipids are going out in the bottom of the box and coming in in the top of the box, since I'm using periodic boundary conditions. This doesn't matter (I think) when running non-constrained simulations, however when I'm constraining the distance between the lipids (pull_geometry=cylinder) and a molecule in the system the system explodes and the simulations crash when the lipids are starting to cross over to the other side. The fact that the system is moving in the box must be the problem since the system explodes exactly when the first lipid passes over to the other side and nothing like this ever happens when the bilayer is not moving in the box. Is there any way to freeze the cylindrical COM of the lipids or something like that so that they stay more or less in the middle of the box all the time? I don't want to use freezegrps and freezedim = N N Y as this freezes the lipids completely in the z direction, and that's not what I want, I want them to be free to move as before but I want to stop the whole system from moving too much in the z direction. Anyone that has experienced a similar problem or know how to go about with this? I would really appreciate any help I can get. Thanks. Emma -- gmx-users mailing listgmx-users@gromacs.orgmailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other way to do this? Otherwise I have to manually translate the system back to its original position in the box after the simulation has crashed and then continue the simulation, but this is not very good since I cannot use the checkpoint file then and the continuation is not exact. Any suggestion what to do? Thanks in advance. Emma Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 27 april 2010 15:37 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Interfacial systems such as membranes can translate independently of surrounding aqueous solvent. Thus, the lipids could move one way, the water can move in the other way, but overall, the net COM motion is zero. If you specify two groups, as Xavier suggested, you treat the COM motion more appropriately. So, more specifically: comm-grps = DPPC_CHOL_MOL SOL ...replacing, of course, whatever your small molecule name where I have MOL. You will need a custom index group created by make_ndx to generate this first group. -Justin Sorry that I didn't understand you explanation. Emma *Från:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] *Skickat:* den 27 april 2010 12:41 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= membrane solvent+ions On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: Hi all! I have a problem regarding lipid bilayer simulations in Gromacs 4. During some of my simulations the whole system is moving in the z direction in the box, meaning that after some time the lipids are going out in the bottom of the box and coming in in the top of the box, since I'm using periodic boundary conditions. This doesn't matter (I think) when running non-constrained simulations, however when I'm constraining the distance between the lipids (pull_geometry=cylinder) and a molecule in the system the system explodes and the simulations crash when the lipids are starting to cross over to the other side. The fact that the system is moving in the box must be the problem since the system explodes exactly when the first lipid passes over to the other side and nothing like this ever happens when the bilayer is not moving in the box. Is there any way to freeze the cylindrical COM of the lipids or something like that so that they stay more or less in the middle of the box all the time? I don't want to use freezegrps and freezedim = N N Y as this freezes the lipids completely in the z direction, and that's not what I want, I want them to be free to move as before but I want to stop the whole system from moving too much in the z direction. Anyone that has
Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
Do you have sufficient water on either side of your membrane? That is, are the lipids crossing PBC because of spurious interactions with the other side of the membrane? That would certainly be a reason for a crash - the model physics is breaking down. How did you generate your initial membrane configuration? -Justin ERIKSSON, EMMA wrote: Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other way to do this? Otherwise I have to manually translate the system back to its original position in the box after the simulation has crashed and then continue the simulation, but this is not very good since I cannot use the checkpoint file then and the continuation is not exact. Any suggestion what to do? Thanks in advance. Emma *Från:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] *Skickat:* den 27 april 2010 16:32 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box you should remove the water and lipid bilayer COM separately. I am not sure what you should do with your small molecule though. Probably best to add it to the bilayer as you constrain their relative position! On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Sorry that I didn't understand you explanation. Emma *Från:* gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl mailto:x.peri...@rug.nl] *Skickat:* den 27 april 2010 12:41 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= membrane solvent+ions On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: Hi all! I have a problem regarding lipid bilayer simulations in Gromacs 4. During some of my simulations the whole system is moving in the z direction in the box, meaning that after some time the lipids are going out in the bottom of the box and coming in in the top of the box, since I'm using periodic boundary conditions. This doesn't matter (I think) when running non-constrained simulations, however when I'm constraining the distance between the lipids (pull_geometry=cylinder) and a molecule in the system the system explodes and the simulations crash when the lipids are starting to cross over to the other side. The fact that the system is moving in the box must be the problem since the system explodes exactly when the first lipid passes over to the other side and nothing like this ever happens when the bilayer is not moving in the box. Is there any way to freeze the cylindrical COM of the lipids or something like that so that they stay more or less in the middle of the box all the time? I don't want to use freezegrps and freezedim = N N Y as this freezes the lipids completely in the z
Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
It is indeed not clear how you system may translate still! Is this translation on the z axis? How much does it move and how quick? On Apr 29, 2010, at 3:09 PM, Justin A. Lemkul wrote: Do you have sufficient water on either side of your membrane? That is, are the lipids crossing PBC because of spurious interactions with the other side of the membrane? That would certainly be a reason for a crash - the model physics is breaking down. How did you generate your initial membrane configuration? -Justin ERIKSSON, EMMA wrote: Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other way to do this? Otherwise I have to manually translate the system back to its original position in the box after the simulation has crashed and then continue the simulation, but this is not very good since I cannot use the checkpoint file then and the continuation is not exact. Any suggestion what to do? Thanks in advance. Emma *Från:* gmx-users-boun...@gromacs.org [gmx-users- boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] *Skickat:* den 27 april 2010 16:32 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box you should remove the water and lipid bilayer COM separately. I am not sure what you should do with your small molecule though. Probably best to add it to the bilayer as you constrain their relative position! On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Sorry that I didn't understand you explanation. Emma *Från:* gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org ] för XAvier Periole [x.peri...@rug.nl mailto:x.peri...@rug.nl] *Skickat:* den 27 april 2010 12:41 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= membrane solvent+ions On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: Hi all! I have a problem regarding lipid bilayer simulations in Gromacs 4. During some of my simulations the whole system is moving in the z direction in the box, meaning that after some time the lipids are going out in the bottom of the box and coming in in the top of the box, since I'm using periodic boundary conditions. This doesn't matter (I think) when running non-constrained simulations, however when I'm constraining the distance between the lipids (pull_geometry=cylinder) and a molecule in the system the system explodes and the simulations crash when the lipids are starting to cross over to the other side. The fact that the system is moving in the box must be the problem since the system explodes exactly when the first lipid passes over to the other side and nothing like this ever happens when the bilayer is not moving in the box. Is there any way to freeze
RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
My system consists of 128 lipids and 3655 water molecules and is one of the structures one can download from University of Calgary. I think that the water phase is thick enough because when I run non-constrained simulations and the system translates there is no crash when the lipids cross the pbc. Emma Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 14:09 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box Do you have sufficient water on either side of your membrane? That is, are the lipids crossing PBC because of spurious interactions with the other side of the membrane? That would certainly be a reason for a crash - the model physics is breaking down. How did you generate your initial membrane configuration? -Justin ERIKSSON, EMMA wrote: Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other way to do this? Otherwise I have to manually translate the system back to its original position in the box after the simulation has crashed and then continue the simulation, but this is not very good since I cannot use the checkpoint file then and the continuation is not exact. Any suggestion what to do? Thanks in advance. Emma *Från:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] *Skickat:* den 27 april 2010 16:32 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box you should remove the water and lipid bilayer COM separately. I am not sure what you should do with your small molecule though. Probably best to add it to the bilayer as you constrain their relative position! On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Sorry that I didn't understand you explanation. Emma *Från:* gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl mailto:x.peri...@rug.nl] *Skickat:* den 27 april 2010 12:41 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= membrane solvent+ions On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: Hi all! I have a problem regarding lipid bilayer simulations in Gromacs 4. During some of my simulations the whole system is moving in the z direction in the box, meaning that after some time the lipids are going out in the bottom of the box and coming in in the top of the box, since I'm using periodic boundary conditions. This doesn't matter (I think) when running non-constrained simulations, however when I'm constraining the distance between the lipids
Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
ERIKSSON, EMMA wrote: My system consists of 128 lipids and 3655 water molecules and is one of the structures one can download from University of Calgary. I think that the water phase is thick enough because when I run non-constrained simulations and the system translates there is no crash when the lipids cross the pbc. What type of pulling are you trying to do? Can you post your .mdp file, or at least your pull parameters? My sense is that your pull distance is greater than half the box dimension in the pull direction, causing lipids to be pulled across PBC and break down. -Justin Emma Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 14:09 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box Do you have sufficient water on either side of your membrane? That is, are the lipids crossing PBC because of spurious interactions with the other side of the membrane? That would certainly be a reason for a crash - the model physics is breaking down. How did you generate your initial membrane configuration? -Justin ERIKSSON, EMMA wrote: Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other way to do this? Otherwise I have to manually translate the system back to its original position in the box after the simulation has crashed and then continue the simulation, but this is not very good since I cannot use the checkpoint file then and the continuation is not exact. Any suggestion what to do? Thanks in advance. Emma *Från:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] *Skickat:* den 27 april 2010 16:32 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box you should remove the water and lipid bilayer COM separately. I am not sure what you should do with your small molecule though. Probably best to add it to the bilayer as you constrain their relative position! On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Sorry that I didn't understand you explanation. Emma *Från:* gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl mailto:x.peri...@rug.nl] *Skickat:* den 27 april 2010 12:41 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= membrane solvent+ions On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: Hi all! I have a problem regarding lipid bilayer simulations in Gromacs 4. During some of my simulations the whole system is moving in the z direction in the box, meaning that after some time the lipids are going out in the
RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
The last section of my mdp file: pull = constraint pull_geometry= cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DPPC pull_group1 = MOL pull_vec1= 0 0 1 pull_init1 = 3.083 comm_mode= linear nstcomm = 1 comm_grps= DPPC_CHOL_MOL SOL With my small molecule being MOL. I'm constraining the distance between the DPPC and the small molecule at different distances along the z direction of the bilayer. This example is for the distance being 3.083 nm between the two groups. The total z box length is ~7.2 nm. Even when I'm running without constraint the system is translating in the z direction but no crash occurs when the pbc is crossed. Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 14:33 Till: Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: My system consists of 128 lipids and 3655 water molecules and is one of the structures one can download from University of Calgary. I think that the water phase is thick enough because when I run non-constrained simulations and the system translates there is no crash when the lipids cross the pbc. What type of pulling are you trying to do? Can you post your .mdp file, or at least your pull parameters? My sense is that your pull distance is greater than half the box dimension in the pull direction, causing lipids to be pulled across PBC and break down. -Justin Emma Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 14:09 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box Do you have sufficient water on either side of your membrane? That is, are the lipids crossing PBC because of spurious interactions with the other side of the membrane? That would certainly be a reason for a crash - the model physics is breaking down. How did you generate your initial membrane configuration? -Justin ERIKSSON, EMMA wrote: Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other way to do this? Otherwise I have to manually translate the system back to its original position in the box after the simulation has crashed and then continue the simulation, but this is not very good since I cannot use the checkpoint file then and the continuation is not exact. Any suggestion what to do? Thanks in advance. Emma *Från:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] *Skickat:* den 27 april 2010 16:32 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box you should remove the water and lipid bilayer COM separately. I am not sure what you should do with your small molecule though. Probably best to add it to the bilayer as you constrain their relative position! On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Sorry that I didn't understand you explanation. Emma
RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
The translation occurs in the z direction, yes. I'm running many constrained simulations but in general the movement of the new simulations, in which the COM translation has been removed for the bilayer and water separately, is about 1 nm in 3 ns. The movement is slower than when I was running the comm-grps = the whole system all together, but the system will still end up crossing the pbc sometime during the simulations. Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r XAvier Periole [x.peri...@rug.nl] Skickat: den 29 april 2010 14:28 Till: jalem...@vt.edu; Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box It is indeed not clear how you system may translate still! Is this translation on the z axis? How much does it move and how quick? On Apr 29, 2010, at 3:09 PM, Justin A. Lemkul wrote: Do you have sufficient water on either side of your membrane? That is, are the lipids crossing PBC because of spurious interactions with the other side of the membrane? That would certainly be a reason for a crash - the model physics is breaking down. How did you generate your initial membrane configuration? -Justin ERIKSSON, EMMA wrote: Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other way to do this? Otherwise I have to manually translate the system back to its original position in the box after the simulation has crashed and then continue the simulation, but this is not very good since I cannot use the checkpoint file then and the continuation is not exact. Any suggestion what to do? Thanks in advance. Emma *Från:* gmx-users-boun...@gromacs.org [gmx-users- boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] *Skickat:* den 27 april 2010 16:32 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box you should remove the water and lipid bilayer COM separately. I am not sure what you should do with your small molecule though. Probably best to add it to the bilayer as you constrain their relative position! On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Sorry that I didn't understand you explanation. Emma *Från:* gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org ] för XAvier Periole [x.peri...@rug.nl mailto:x.peri...@rug.nl] *Skickat:* den 27 april 2010 12:41 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= membrane solvent+ions On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: Hi all! I have
Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
ERIKSSON, EMMA wrote: The last section of my mdp file: pull = constraint pull_geometry= cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DPPC pull_group1 = MOL pull_vec1= 0 0 1 pull_init1 = 3.083 comm_mode= linear nstcomm = 1 comm_grps = DPPC_CHOL_MOL SOL With my small molecule being MOL. I'm constraining the distance between the DPPC and the small molecule at different distances along the z direction of the bilayer. This example is for the distance being 3.083 nm between the two groups. The total z box length is ~7.2 nm. Even when I'm running without constraint the system is translating in the z direction but no crash occurs when the pbc is crossed. At this point, it would probably be useful to understand how you set up and build the system. The original 128-lipid DPPC from Tieleman is ~6.5 nm in the z-dimension, so somewhere along the way you've picked up 0.7 nm. Is there void space in your box? Did you remove the water and re-solvate? There is no reason (in my mind) why the bilayer should be translating in the z-dimension at all. I've done a number of simulations with this particular DPPC bilayer and never had a problem. Maybe you can also post your whole .mdp file to see if there are any problems. -Justin Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 14:33 Till: Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: My system consists of 128 lipids and 3655 water molecules and is one of the structures one can download from University of Calgary. I think that the water phase is thick enough because when I run non-constrained simulations and the system translates there is no crash when the lipids cross the pbc. What type of pulling are you trying to do? Can you post your .mdp file, or at least your pull parameters? My sense is that your pull distance is greater than half the box dimension in the pull direction, causing lipids to be pulled across PBC and break down. -Justin Emma Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 14:09 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box Do you have sufficient water on either side of your membrane? That is, are the lipids crossing PBC because of spurious interactions with the other side of the membrane? That would certainly be a reason for a crash - the model physics is breaking down. How did you generate your initial membrane configuration? -Justin ERIKSSON, EMMA wrote: Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other way to do this? Otherwise I have to manually translate the system back to its original position in the box after the simulation has crashed and then continue the simulation, but this is not very good since I cannot use the checkpoint file then and the continuation is not exact. Any suggestion what to do? Thanks in advance. Emma *Från:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] *Skickat:* den 27 april 2010 16:32 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box you should remove the water and lipid bilayer COM separately. I am not sure what you should do with your small molecule though. Probably best to add it to the bilayer as you constrain their relative position! On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my
RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
The increase in z box length is due to that I have replaced 12 DPPC lipids by cholesterol molecules. Cholesterol reduces the area per lipid and compresses the bilayer lateral (xy) area, resulting in a slight increase in the water layer thickness. I have performed exactly the same simulations with a higher concentration of cholesterol (in which the bilayer is even more compressed and the water phase therefore is even thicker) and there is no translation in any of the simulations. Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 15:28 Till: Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: The last section of my mdp file: pull = constraint pull_geometry= cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DPPC pull_group1 = MOL pull_vec1= 0 0 1 pull_init1 = 3.083 comm_mode= linear nstcomm = 1 comm_grps = DPPC_CHOL_MOL SOL With my small molecule being MOL. I'm constraining the distance between the DPPC and the small molecule at different distances along the z direction of the bilayer. This example is for the distance being 3.083 nm between the two groups. The total z box length is ~7.2 nm. Even when I'm running without constraint the system is translating in the z direction but no crash occurs when the pbc is crossed. At this point, it would probably be useful to understand how you set up and build the system. The original 128-lipid DPPC from Tieleman is ~6.5 nm in the z-dimension, so somewhere along the way you've picked up 0.7 nm. Is there void space in your box? Did you remove the water and re-solvate? There is no reason (in my mind) why the bilayer should be translating in the z-dimension at all. I've done a number of simulations with this particular DPPC bilayer and never had a problem. Maybe you can also post your whole .mdp file to see if there are any problems. -Justin Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 14:33 Till: Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: My system consists of 128 lipids and 3655 water molecules and is one of the structures one can download from University of Calgary. I think that the water phase is thick enough because when I run non-constrained simulations and the system translates there is no crash when the lipids cross the pbc. What type of pulling are you trying to do? Can you post your .mdp file, or at least your pull parameters? My sense is that your pull distance is greater than half the box dimension in the pull direction, causing lipids to be pulled across PBC and break down. -Justin Emma Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 14:09 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box Do you have sufficient water on either side of your membrane? That is, are the lipids crossing PBC because of spurious interactions with the other side of the membrane? That would certainly be a reason for a crash - the model physics is breaking down. How did you generate your initial membrane configuration? -Justin ERIKSSON, EMMA wrote: Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other way to do this? Otherwise I have to manually translate the system back to its original position in the box after the simulation has crashed and then continue the simulation, but this is not very good since I cannot use the checkpoint file then and the continuation is not exact. Any suggestion what to do? Thanks in advance. Emma *Från:*
Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
ERIKSSON, EMMA wrote: The increase in z box length is due to that I have replaced 12 DPPC lipids by cholesterol molecules. Cholesterol reduces the area per lipid and compresses the bilayer lateral (xy) area, resulting in a slight increase in the water layer thickness. I have performed exactly the same simulations with a higher concentration of cholesterol (in which the bilayer is even more compressed and the water phase therefore is even thicker) and there is no translation in any of the simulations. So if I understand correctly, you have different levels of cholesterol in DPPC, and at low cholesterol concentration you get a z-translation of your membrane, but at high concentration of cholesterol, you get no translation at all? Can you plot (using g_traj -com) the motion of the membrane to quantify just how much the membrane is moving? And again I would ask that you post your entire .mdp file, just to see your settings. -Justin Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 15:28 Till: Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: The last section of my mdp file: pull = constraint pull_geometry= cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DPPC pull_group1 = MOL pull_vec1= 0 0 1 pull_init1 = 3.083 comm_mode= linear nstcomm = 1 comm_grps = DPPC_CHOL_MOL SOL With my small molecule being MOL. I'm constraining the distance between the DPPC and the small molecule at different distances along the z direction of the bilayer. This example is for the distance being 3.083 nm between the two groups. The total z box length is ~7.2 nm. Even when I'm running without constraint the system is translating in the z direction but no crash occurs when the pbc is crossed. At this point, it would probably be useful to understand how you set up and build the system. The original 128-lipid DPPC from Tieleman is ~6.5 nm in the z-dimension, so somewhere along the way you've picked up 0.7 nm. Is there void space in your box? Did you remove the water and re-solvate? There is no reason (in my mind) why the bilayer should be translating in the z-dimension at all. I've done a number of simulations with this particular DPPC bilayer and never had a problem. Maybe you can also post your whole .mdp file to see if there are any problems. -Justin Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 14:33 Till: Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: My system consists of 128 lipids and 3655 water molecules and is one of the structures one can download from University of Calgary. I think that the water phase is thick enough because when I run non-constrained simulations and the system translates there is no crash when the lipids cross the pbc. What type of pulling are you trying to do? Can you post your .mdp file, or at least your pull parameters? My sense is that your pull distance is greater than half the box dimension in the pull direction, causing lipids to be pulled across PBC and break down. -Justin Emma Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 14:09 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box Do you have sufficient water on either side of your membrane? That is, are the lipids crossing PBC because of spurious interactions with the other side of the membrane? That would certainly be a reason for a crash - the model physics is breaking down. How did you generate your initial membrane configuration? -Justin ERIKSSON, EMMA wrote: Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other
Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
Well 1 nm / 3 ns is definitely not reasonable! That is about 1 m / s ... 3.6 km/h We has seen motion of the COM of a bilayer using CG models but the motions were ~ 0.1 nm on the mircosecond timescale! This is due to the way COM is removed ... not exact but appears only on large time scales. On Apr 29, 2010, at 4:23 PM, ERIKSSON, EMMA wrote: The translation occurs in the z direction, yes. I'm running many constrained simulations but in general the movement of the new simulations, in which the COM translation has been removed for the bilayer and water separately, is about 1 nm in 3 ns. The movement is slower than when I was running the comm-grps = the whole system all together, but the system will still end up crossing the pbc sometime during the simulations. Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r XAvier Periole [x.peri...@rug.nl] Skickat: den 29 april 2010 14:28 Till: jalem...@vt.edu; Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box It is indeed not clear how you system may translate still! Is this translation on the z axis? How much does it move and how quick? On Apr 29, 2010, at 3:09 PM, Justin A. Lemkul wrote: Do you have sufficient water on either side of your membrane? That is, are the lipids crossing PBC because of spurious interactions with the other side of the membrane? That would certainly be a reason for a crash - the model physics is breaking down. How did you generate your initial membrane configuration? -Justin ERIKSSON, EMMA wrote: Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other way to do this? Otherwise I have to manually translate the system back to its original position in the box after the simulation has crashed and then continue the simulation, but this is not very good since I cannot use the checkpoint file then and the continuation is not exact. Any suggestion what to do? Thanks in advance. Emma *Från:* gmx-users-boun...@gromacs.org [gmx-users- boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] *Skickat:* den 27 april 2010 16:32 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box you should remove the water and lipid bilayer COM separately. I am not sure what you should do with your small molecule though. Probably best to add it to the bilayer as you constrain their relative position! On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Sorry that I didn't understand you explanation. Emma *Från:* gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org ] för XAvier Periole [x.peri...@rug.nl mailto:x.peri...@rug.nl] *Skickat:* den 27 april 2010 12:41 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of
RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
Justin, you understood it correctly; I only have problems with the low cholesterol concentration. According to g_traj -com the COM of DPPC in one of the simulations moves 0.6 nm in 3.5 ns. And as Xavier just wrote it's quite much... My mdp file looks like this: title= dppc128 cpp = /lib/cpp include = define = integrator = md dt = 0.002 nsteps = 350 ; 7 ns nstlog = 25000 nstenergy= 25 nstxout = 75 nstxtcout= 400 nstvout = 75 nstfout = 0 xtc_grps = DPPC SOL CHOL MOL energygrps = DPPC SOL CHOL MOL nstlist = 10 ns_type = grid rlist= 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = Cut-off rvdw = 1.0 tcoupl = Nose-hoover tc-grps = DPPC SOL CHOL MOL tau_t= 0.1 0.1 0.1 0.1 ref_t= 323 323 323 323 Pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p= 1.0 1.0e-14 compressibility = 4.5e-5 4.5e-15 ref_p= 1.0 1.0 gen_vel = yes gen_temp = 323 gen_seed = 173529 constraints = all-bonds pbc = xyz optimize_fft = yes unconstrained_start = no pull = constraint pull_geometry= cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DPPC pull_group1 = MOL pull_vec1= 0 0 1 pull_init1 = 3.498 comm_mode= linear nstcomm = 1 comm_grps= DPPC_CHOL_MOL SOL Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 15:44 Till: Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: The increase in z box length is due to that I have replaced 12 DPPC lipids by cholesterol molecules. Cholesterol reduces the area per lipid and compresses the bilayer lateral (xy) area, resulting in a slight increase in the water layer thickness. I have performed exactly the same simulations with a higher concentration of cholesterol (in which the bilayer is even more compressed and the water phase therefore is even thicker) and there is no translation in any of the simulations. So if I understand correctly, you have different levels of cholesterol in DPPC, and at low cholesterol concentration you get a z-translation of your membrane, but at high concentration of cholesterol, you get no translation at all? Can you plot (using g_traj -com) the motion of the membrane to quantify just how much the membrane is moving? And again I would ask that you post your entire .mdp file, just to see your settings. -Justin Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 15:28 Till: Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: The last section of my mdp file: pull = constraint pull_geometry= cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DPPC pull_group1 = MOL pull_vec1= 0 0 1 pull_init1 = 3.083 comm_mode= linear nstcomm = 1 comm_grps = DPPC_CHOL_MOL SOL With my small molecule being MOL. I'm constraining the distance between the DPPC and the small molecule at different distances along the z direction of the bilayer. This example is for the distance being 3.083 nm between the two groups. The total z box length is ~7.2 nm. Even when I'm running without constraint the system is translating in the z direction but no crash occurs when the pbc is crossed. At this point, it would probably be useful to understand how you set up and build the system. The original 128-lipid DPPC from Tieleman is ~6.5 nm in the z-dimension, so somewhere along the way you've picked up 0.7 nm. Is there void space in your box? Did you remove the water and re-solvate? There is no reason (in my mind) why the
Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
ERIKSSON, EMMA wrote: Pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p= 1.0 1.0e-14 compressibility = 4.5e-5 4.5e-15 I would bet almost anything that this is the cause of your problem. How did you come up with these bizarre values for tau_p and compressibility in the z-dimension? I recall another post where there was an issue of z-drift like this one. You're using a tau_p in the z-dimension of 1.0x10e-14 ps - I don't even see how that's possible! It is certainly far too strenuous for P-R coupling, where you should probably be using tau_p on the order of 5-10 ps. The compressibility also doesn't make any sense to me. 4.5e-5 in all dimensions should suffice. -Justin ref_p= 1.0 1.0 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.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] Constrained simulations crash when bilayer moves in the z direction in the box
ERIKSSON, EMMA wrote: I was using those strange values of tau_p and compressibility to keep the z box length fixed in order to avoid problems associated with scaling the positions of the molecules in the box when we constrain the distance between DPPC and the small molecule. I was told to use those values but maybe it's not correct... I would certainly try to eliminate it as a possibility. I just don't know how the pressure coupling algorithm could possibly handle a tau_t that is several 10e-11 times smaller than the timestep! A well-equilibrated system should not fluctuate substantially over the course of a simulation, anyway. But if you need to fix the box, you *may* be able to set the relevant values of tau_t and compressibility to zero (as in the case of tau_t for temperature coupling), but I have never tried it. -Justin Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 17:20 Till: Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: Pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p= 1.0 1.0e-14 compressibility = 4.5e-5 4.5e-15 I would bet almost anything that this is the cause of your problem. How did you come up with these bizarre values for tau_p and compressibility in the z-dimension? I recall another post where there was an issue of z-drift like this one. You're using a tau_p in the z-dimension of 1.0x10e-14 ps - I don't even see how that's possible! It is certainly far too strenuous for P-R coupling, where you should probably be using tau_p on the order of 5-10 ps. The compressibility also doesn't make any sense to me. 4.5e-5 in all dimensions should suffice. -Justin ref_p= 1.0 1.0 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 list gmx-users@gromacs.org http://lists.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 MILES-IGERT Trainee 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://lists.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] Constrained simulations crash when bilayer moves in the z direction in the box
Justin A. Lemkul wrote: ERIKSSON, EMMA wrote: I was using those strange values of tau_p and compressibility to keep the z box length fixed in order to avoid problems associated with scaling the positions of the molecules in the box when we constrain the distance between DPPC and the small molecule. I was told to use those values but maybe it's not correct... I would certainly try to eliminate it as a possibility. I just don't know how the pressure coupling algorithm could possibly handle a tau_t that is several 10e-11 times smaller than the timestep! *Edit* That should read tau_p. A well-equilibrated system should not fluctuate substantially over the course of a simulation, anyway. But if you need to fix the box, you *may* be able to set the relevant values of tau_t and compressibility to *Edit* This should also read tau_p. zero (as in the case of tau_t for temperature coupling), but I have never tried it. This one's right :) Apologies for any confusion, my brain was going faster than my fingers on this reply! -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.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] Constrained simulations crash when bilayer moves in the z direction in the box
The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= membrane solvent+ions On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: Hi all! I have a problem regarding lipid bilayer simulations in Gromacs 4. During some of my simulations the whole system is moving in the z direction in the box, meaning that after some time the lipids are going out in the bottom of the box and coming in in the top of the box, since I'm using periodic boundary conditions. This doesn't matter (I think) when running non-constrained simulations, however when I'm constraining the distance between the lipids (pull_geometry=cylinder) and a molecule in the system the system explodes and the simulations crash when the lipids are starting to cross over to the other side. The fact that the system is moving in the box must be the problem since the system explodes exactly when the first lipid passes over to the other side and nothing like this ever happens when the bilayer is not moving in the box. Is there any way to freeze the cylindrical COM of the lipids or something like that so that they stay more or less in the middle of the box all the time? I don't want to use freezegrps and freezedim = N N Y as this freezes the lipids completely in the z direction, and that's not what I want, I want them to be free to move as before but I want to stop the whole system from moving too much in the z direction. Anyone that has experienced a similar problem or know how to go about with this? I would really appreciate any help I can get. Thanks. Emma -- gmx-users mailing listgmx-users@gromacs.org http://lists.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://lists.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] Constrained simulations crash when bilayer moves in the z direction in the box
Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Sorry that I didn't understand you explanation. Emma Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] Skickat: den 27 april 2010 12:41 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= membrane solvent+ions On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: Hi all! I have a problem regarding lipid bilayer simulations in Gromacs 4. During some of my simulations the whole system is moving in the z direction in the box, meaning that after some time the lipids are going out in the bottom of the box and coming in in the top of the box, since I'm using periodic boundary conditions. This doesn't matter (I think) when running non-constrained simulations, however when I'm constraining the distance between the lipids (pull_geometry=cylinder) and a molecule in the system the system explodes and the simulations crash when the lipids are starting to cross over to the other side. The fact that the system is moving in the box must be the problem since the system explodes exactly when the first lipid passes over to the other side and nothing like this ever happens when the bilayer is not moving in the box. Is there any way to freeze the cylindrical COM of the lipids or something like that so that they stay more or less in the middle of the box all the time? I don't want to use freezegrps and freezedim = N N Y as this freezes the lipids completely in the z direction, and that's not what I want, I want them to be free to move as before but I want to stop the whole system from moving too much in the z direction. Anyone that has experienced a similar problem or know how to go about with this? I would really appreciate any help I can get. Thanks. Emma -- gmx-users mailing listgmx-users@gromacs.orgmailto:gmx-users@gromacs.org http://lists.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.orgmailto: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://lists.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] Constrained simulations crash when bilayer moves in the z direction in the box
ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Interfacial systems such as membranes can translate independently of surrounding aqueous solvent. Thus, the lipids could move one way, the water can move in the other way, but overall, the net COM motion is zero. If you specify two groups, as Xavier suggested, you treat the COM motion more appropriately. So, more specifically: comm-grps = DPPC_CHOL_MOL SOL ...replacing, of course, whatever your small molecule name where I have MOL. You will need a custom index group created by make_ndx to generate this first group. -Justin Sorry that I didn't understand you explanation. Emma *Från:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] *Skickat:* den 27 april 2010 12:41 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= membrane solvent+ions On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: Hi all! I have a problem regarding lipid bilayer simulations in Gromacs 4. During some of my simulations the whole system is moving in the z direction in the box, meaning that after some time the lipids are going out in the bottom of the box and coming in in the top of the box, since I'm using periodic boundary conditions. This doesn't matter (I think) when running non-constrained simulations, however when I'm constraining the distance between the lipids (pull_geometry=cylinder) and a molecule in the system the system explodes and the simulations crash when the lipids are starting to cross over to the other side. The fact that the system is moving in the box must be the problem since the system explodes exactly when the first lipid passes over to the other side and nothing like this ever happens when the bilayer is not moving in the box. Is there any way to freeze the cylindrical COM of the lipids or something like that so that they stay more or less in the middle of the box all the time? I don't want to use freezegrps and freezedim = N N Y as this freezes the lipids completely in the z direction, and that's not what I want, I want them to be free to move as before but I want to stop the whole system from moving too much in the z direction. Anyone that has experienced a similar problem or know how to go about with this? I would really appreciate any help I can get. Thanks. Emma -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 mailto: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 MILES-IGERT Trainee 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://lists.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
Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
you should remove the water and lipid bilayer COM separately. I am not sure what you should do with your small molecule though. Probably best to add it to the bilayer as you constrain their relative position! On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Sorry that I didn't understand you explanation. Emma Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] Skickat: den 27 april 2010 12:41 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= membrane solvent+ions On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: Hi all! I have a problem regarding lipid bilayer simulations in Gromacs 4. During some of my simulations the whole system is moving in the z direction in the box, meaning that after some time the lipids are going out in the bottom of the box and coming in in the top of the box, since I'm using periodic boundary conditions. This doesn't matter (I think) when running non-constrained simulations, however when I'm constraining the distance between the lipids (pull_geometry=cylinder) and a molecule in the system the system explodes and the simulations crash when the lipids are starting to cross over to the other side. The fact that the system is moving in the box must be the problem since the system explodes exactly when the first lipid passes over to the other side and nothing like this ever happens when the bilayer is not moving in the box. Is there any way to freeze the cylindrical COM of the lipids or something like that so that they stay more or less in the middle of the box all the time? I don't want to use freezegrps and freezedim = N N Y as this freezes the lipids completely in the z direction, and that's not what I want, I want them to be free to move as before but I want to stop the whole system from moving too much in the z direction. Anyone that has experienced a similar problem or know how to go about with this? I would really appreciate any help I can get. Thanks. Emma -- gmx-users mailing listgmx-users@gromacs.org http://lists.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://lists.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://lists.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
