Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault)
On 7/10/15 7:15 PM, Nathan K Houtz wrote: Actually, I think I found the problem. When i looked at the pdb files in vmd the first time I missed it, but a colleague had a hunch and I found that he was right! I think that shake is constraining atoms to the wrong molecules. Here's a screenshot I took where you can see what I mean:http://imgur.com/1bgThDv Sorry, this doesn't make sense to me. Constraints are applied per-moleculetype; they cannot be applied between molecules. I can't tell anything from this image. I'm still not sure how to fix it though. The molecule numbering in my .gro file is correct, and there are only 4 atoms per molecule (or 3 plus the dummy). How can I tell shake to look at each molecule individually? Or have I made a mistake somewhere? Here are my most recent files: .gro file: (only part of it -- there is a character limit. this is the first and last ten molecules with the box dimensions at the bottom) http://textuploader.com/e898 topology file: http://textuploader.com/e89g minimization: http://textuploader.com/e8rc .mdp file: http://textuploader.com/e896 log file from a failed simulation: http://textuploader.com/e80y Thanks for your help! If you do still want the full .gro file to run the simulation, I can look for a different file host. I really would like a nice tarball with everything so that I can play with it a bit. That's the only way I'm going to have any chance of figuring it out. I would also dispute your previous assertion that the temperature is fine - it goes out of control immediately :) -Justin Nathan - Original Message - From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Sent: Friday, July 10, 2015 5:06:34 PM Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault) On 7/9/15 9:23 PM, Nathan K Houtz wrote: Thanks for your explanations, Dr. Lemkul. I had already corrected a couple of the things you suggested. Gromacs won't actually let me run with Nose-Hoover and Parrinello-Rahman together (or at least, it gives a warning not to do that and stops). I'd like to run in NVT anyway, so I had set Pcoupl to 'no'. I had also increased the cutoffs and my nstlist is 20. I have now also changed the tcoupl to v-rescale, but unfortunately that alone didn't help. So I'm not sure exactly what I can inspect to find the source of my error. I know that temperature, pressure, and total energy are all warning signs of bad things if they misbehave, but they were all fairly constant throughout the simulation. (This is for the flexible-model simulation:) The starting energy for 1700 water molecules at 120K was -1.08744e+05, and it finished at -1.06047e+05 with no significant variations on any step. Pressure and temperature were also fine. I attempted to look at the results visually in vmd but I might have done something wrong because the .trr file has some error in it and vmd crashes. But the starting geometry after minimization looks fine: none of the molecules were moved out of their position in the crystal. For the constrained molecules, the energy stays about the same (about -1e+5) for the first 8 timesteps and then quickly blows up to +2e15 at step 12 before it obviously fails. I get shake warnings from step 0 though. In vmd, the first 8 steps look reasonable (checking the .pdb files that gromacs outputs when there are warnings) and all the molecules seem to hold their places in the crystal, but then at step 9 suddenly some of the molecules become misshapen with very long or very short bonds. Of course it goes downhill from there, but I can't figure out what's causing the problems since it's clearly happening from the very beginning (according to the shake warnings). What other things could I look at to troubleshoot my problem? Not sure, but at least the failure happens fast. Upload all your input files somewhere and I'll take a few minutes to see if I can spot anything. -Justin Thanks for your help, Nathan - Original Message - From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Sent: Thursday, July 9, 2015 7:39:47 AM Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault) On 7/8/15 8:06 PM, Nathan K Houtz wrote: Hello, I deleted the email and can't respond to my last reply directly - sorry! I got this response from Mark Abraham: Hi, Try doing some EM and initial equilibration with no constraints at all, perhaps? Mark I tried commenting out the shake commands, and got a short (5000 step) simulation to run just fine without blowing up. Before, I would get shake warnings from the first few steps and a segmentation fault around step 13 or 14. I would like to be able to simulate with rigid molecules, though. Why would the simulation work with flexible molecules but not rigid ones? Flexible water allows weird geometry, which is probably coming
Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault)
On 7/10/15 7:21 PM, Justin Lemkul wrote: On 7/10/15 7:15 PM, Nathan K Houtz wrote: Actually, I think I found the problem. When i looked at the pdb files in vmd the first time I missed it, but a colleague had a hunch and I found that he was right! I think that shake is constraining atoms to the wrong molecules. Here's a screenshot I took where you can see what I mean:http://imgur.com/1bgThDv Sorry, this doesn't make sense to me. Constraints are applied per-moleculetype; they cannot be applied between molecules. I can't tell anything from this image. I'm still not sure how to fix it though. The molecule numbering in my .gro file is correct, and there are only 4 atoms per molecule (or 3 plus the dummy). How can I tell shake to look at each molecule individually? Or have I made a mistake somewhere? Here are my most recent files: .gro file: (only part of it -- there is a character limit. this is the first and last ten molecules with the box dimensions at the bottom) http://textuploader.com/e898 topology file: http://textuploader.com/e89g minimization: http://textuploader.com/e8rc .mdp file: http://textuploader.com/e896 One final thing after I took another look on a hunch - constraining all angles is very unstable, and doing it with SHAKE is (I think) even worse. You've got [constraints] manually defined in the topology to keep the geometry rigid; you should set constraints = none to just use those constraints specified in the topology. -Justin log file from a failed simulation: http://textuploader.com/e80y Thanks for your help! If you do still want the full .gro file to run the simulation, I can look for a different file host. I really would like a nice tarball with everything so that I can play with it a bit. That's the only way I'm going to have any chance of figuring it out. I would also dispute your previous assertion that the temperature is fine - it goes out of control immediately :) -Justin Nathan - Original Message - From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Sent: Friday, July 10, 2015 5:06:34 PM Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault) On 7/9/15 9:23 PM, Nathan K Houtz wrote: Thanks for your explanations, Dr. Lemkul. I had already corrected a couple of the things you suggested. Gromacs won't actually let me run with Nose-Hoover and Parrinello-Rahman together (or at least, it gives a warning not to do that and stops). I'd like to run in NVT anyway, so I had set Pcoupl to 'no'. I had also increased the cutoffs and my nstlist is 20. I have now also changed the tcoupl to v-rescale, but unfortunately that alone didn't help. So I'm not sure exactly what I can inspect to find the source of my error. I know that temperature, pressure, and total energy are all warning signs of bad things if they misbehave, but they were all fairly constant throughout the simulation. (This is for the flexible-model simulation:) The starting energy for 1700 water molecules at 120K was -1.08744e+05, and it finished at -1.06047e+05 with no significant variations on any step. Pressure and temperature were also fine. I attempted to look at the results visually in vmd but I might have done something wrong because the .trr file has some error in it and vmd crashes. But the starting geometry after minimization looks fine: none of the molecules were moved out of their position in the crystal. For the constrained molecules, the energy stays about the same (about -1e+5) for the first 8 timesteps and then quickly blows up to +2e15 at step 12 before it obviously fails. I get shake warnings from step 0 though. In vmd, the first 8 steps look reasonable (checking the .pdb files that gromacs outputs when there are warnings) and all the molecules seem to hold their places in the crystal, but then at step 9 suddenly some of the molecules become misshapen with very long or very short bonds. Of course it goes downhill from there, but I can't figure out what's causing the problems since it's clearly happening from the very beginning (according to the shake warnings). What other things could I look at to troubleshoot my problem? Not sure, but at least the failure happens fast. Upload all your input files somewhere and I'll take a few minutes to see if I can spot anything. -Justin Thanks for your help, Nathan - Original Message - From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Sent: Thursday, July 9, 2015 7:39:47 AM Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault) On 7/8/15 8:06 PM, Nathan K Houtz wrote: Hello, I deleted the email and can't respond to my last reply directly - sorry! I got this response from Mark Abraham: Hi, Try doing some EM and initial equilibration with no constraints at all, perhaps? Mark I tried commenting out the shake commands, and got a short (5000 step) simulation
Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault)
Hi, Sorry, I mean your [molecules] section. The order there, and the atom orders looked up from [moleculetypes] imply the required atom ordering for a matching .gro. Run grompp and see what it says. Mark On Sat, Jul 11, 2015 at 3:27 AM Nathan K Houtz nho...@purdue.edu wrote: Hi, Thanks Mark. I'm sorry though, I don't think I understand what you mean. I thought the [system] section of the topology file was just a name for the system. How should I imply an order for the atoms? I did double check that the ordering in atoms is the same as it is in my .gro file (grommp -c input). 'OW', 'HW', 'HW', then 'DW' - Original Message - From: Mark Abraham mark.j.abra...@gmail.com To: gmx-us...@gromacs.org Sent: Friday, July 10, 2015 7:24:49 PM Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault) Hi, That could only happen if your grompp -c input used a different atom ordering from that implied by your [system] section of your .top. grompp warns about this, but maybe you didn't notice... (Or the structure you loaded into VMD is a mismatch to the trajectory, so its heuristics for guessing where bonds actually are get double-crossed.) Mark On Sat, Jul 11, 2015 at 1:15 AM Nathan K Houtz nho...@purdue.edu wrote: Actually, I think I found the problem. When i looked at the pdb files in vmd the first time I missed it, but a colleague had a hunch and I found that he was right! I think that shake is constraining atoms to the wrong molecules. Here's a screenshot I took where you can see what I mean: http://imgur.com/1bgThDv I'm still not sure how to fix it though. The molecule numbering in my .gro file is correct, and there are only 4 atoms per molecule (or 3 plus the dummy). How can I tell shake to look at each molecule individually? Or have I made a mistake somewhere? Here are my most recent files: .gro file: (only part of it -- there is a character limit. this is the first and last ten molecules with the box dimensions at the bottom) http://textuploader.com/e898 topology file: http://textuploader.com/e89g minimization: http://textuploader.com/e8rc .mdp file: http://textuploader.com/e896 log file from a failed simulation: http://textuploader.com/e80y Thanks for your help! If you do still want the full .gro file to run the simulation, I can look for a different file host. Nathan - Original Message - From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Sent: Friday, July 10, 2015 5:06:34 PM Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault) On 7/9/15 9:23 PM, Nathan K Houtz wrote: Thanks for your explanations, Dr. Lemkul. I had already corrected a couple of the things you suggested. Gromacs won't actually let me run with Nose-Hoover and Parrinello-Rahman together (or at least, it gives a warning not to do that and stops). I'd like to run in NVT anyway, so I had set Pcoupl to 'no'. I had also increased the cutoffs and my nstlist is 20. I have now also changed the tcoupl to v-rescale, but unfortunately that alone didn't help. So I'm not sure exactly what I can inspect to find the source of my error. I know that temperature, pressure, and total energy are all warning signs of bad things if they misbehave, but they were all fairly constant throughout the simulation. (This is for the flexible-model simulation:) The starting energy for 1700 water molecules at 120K was -1.08744e+05, and it finished at -1.06047e+05 with no significant variations on any step. Pressure and temperature were also fine. I attempted to look at the results visually in vmd but I might have done something wrong because the .trr file has some error in it and vmd crashes. But the starting geometry after minimization looks fine: none of the molecules were moved out of their position in the crystal. For the constrained molecules, the energy stays about the same (about -1e+5) for the first 8 timesteps and then quickly blows up to +2e15 at step 12 before it obviously fails. I get shake warnings from step 0 though. In vmd, the first 8 steps look reasonable (checking the .pdb files that gromacs outputs when there are warnings) and all the molecules seem to hold their places in the crystal, but then at step 9 suddenly some of the molecules become misshapen with very long or very short bonds. Of course it goes downhill from there, but I can't figure out what's causing the problems since it's clearly happening from the very beginning (according to the shake warnings). What other things could I look at to troubleshoot my problem? Not sure, but at least the failure happens fast. Upload all your input files somewhere and I'll take a few minutes to see if I can spot anything. -Justin Thanks for your
Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault)
Hi, Thanks Mark. I'm sorry though, I don't think I understand what you mean. I thought the [system] section of the topology file was just a name for the system. How should I imply an order for the atoms? I did double check that the ordering in atoms is the same as it is in my .gro file (grommp -c input). 'OW', 'HW', 'HW', then 'DW' - Original Message - From: Mark Abraham mark.j.abra...@gmail.com To: gmx-us...@gromacs.org Sent: Friday, July 10, 2015 7:24:49 PM Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault) Hi, That could only happen if your grompp -c input used a different atom ordering from that implied by your [system] section of your .top. grompp warns about this, but maybe you didn't notice... (Or the structure you loaded into VMD is a mismatch to the trajectory, so its heuristics for guessing where bonds actually are get double-crossed.) Mark On Sat, Jul 11, 2015 at 1:15 AM Nathan K Houtz nho...@purdue.edu wrote: Actually, I think I found the problem. When i looked at the pdb files in vmd the first time I missed it, but a colleague had a hunch and I found that he was right! I think that shake is constraining atoms to the wrong molecules. Here's a screenshot I took where you can see what I mean: http://imgur.com/1bgThDv I'm still not sure how to fix it though. The molecule numbering in my .gro file is correct, and there are only 4 atoms per molecule (or 3 plus the dummy). How can I tell shake to look at each molecule individually? Or have I made a mistake somewhere? Here are my most recent files: .gro file: (only part of it -- there is a character limit. this is the first and last ten molecules with the box dimensions at the bottom) http://textuploader.com/e898 topology file: http://textuploader.com/e89g minimization: http://textuploader.com/e8rc .mdp file: http://textuploader.com/e896 log file from a failed simulation: http://textuploader.com/e80y Thanks for your help! If you do still want the full .gro file to run the simulation, I can look for a different file host. Nathan - Original Message - From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Sent: Friday, July 10, 2015 5:06:34 PM Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault) On 7/9/15 9:23 PM, Nathan K Houtz wrote: Thanks for your explanations, Dr. Lemkul. I had already corrected a couple of the things you suggested. Gromacs won't actually let me run with Nose-Hoover and Parrinello-Rahman together (or at least, it gives a warning not to do that and stops). I'd like to run in NVT anyway, so I had set Pcoupl to 'no'. I had also increased the cutoffs and my nstlist is 20. I have now also changed the tcoupl to v-rescale, but unfortunately that alone didn't help. So I'm not sure exactly what I can inspect to find the source of my error. I know that temperature, pressure, and total energy are all warning signs of bad things if they misbehave, but they were all fairly constant throughout the simulation. (This is for the flexible-model simulation:) The starting energy for 1700 water molecules at 120K was -1.08744e+05, and it finished at -1.06047e+05 with no significant variations on any step. Pressure and temperature were also fine. I attempted to look at the results visually in vmd but I might have done something wrong because the .trr file has some error in it and vmd crashes. But the starting geometry after minimization looks fine: none of the molecules were moved out of their position in the crystal. For the constrained molecules, the energy stays about the same (about -1e+5) for the first 8 timesteps and then quickly blows up to +2e15 at step 12 before it obviously fails. I get shake warnings from step 0 though. In vmd, the first 8 steps look reasonable (checking the .pdb files that gromacs outputs when there are warnings) and all the molecules seem to hold their places in the crystal, but then at step 9 suddenly some of the molecules become misshapen with very long or very short bonds. Of course it goes downhill from there, but I can't figure out what's causing the problems since it's clearly happening from the very beginning (according to the shake warnings). What other things could I look at to troubleshoot my problem? Not sure, but at least the failure happens fast. Upload all your input files somewhere and I'll take a few minutes to see if I can spot anything. -Justin Thanks for your help, Nathan - Original Message - From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Sent: Thursday, July 9, 2015 7:39:47 AM Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault) On 7/8/15 8:06 PM, Nathan K Houtz wrote: Hello, I deleted the email and can't respond to my last
Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault)
On 7/9/15 9:23 PM, Nathan K Houtz wrote: Thanks for your explanations, Dr. Lemkul. I had already corrected a couple of the things you suggested. Gromacs won't actually let me run with Nose-Hoover and Parrinello-Rahman together (or at least, it gives a warning not to do that and stops). I'd like to run in NVT anyway, so I had set Pcoupl to 'no'. I had also increased the cutoffs and my nstlist is 20. I have now also changed the tcoupl to v-rescale, but unfortunately that alone didn't help. So I'm not sure exactly what I can inspect to find the source of my error. I know that temperature, pressure, and total energy are all warning signs of bad things if they misbehave, but they were all fairly constant throughout the simulation. (This is for the flexible-model simulation:) The starting energy for 1700 water molecules at 120K was -1.08744e+05, and it finished at -1.06047e+05 with no significant variations on any step. Pressure and temperature were also fine. I attempted to look at the results visually in vmd but I might have done something wrong because the .trr file has some error in it and vmd crashes. But the starting geometry after minimization looks fine: none of the molecules were moved out of their position in the crystal. For the constrained molecules, the energy stays about the same (about -1e+5) for the first 8 timesteps and then quickly blows up to +2e15 at step 12 before it obviously fails. I get shake warnings from step 0 though. In vmd, the first 8 steps look reasonable (checking the .pdb files that gromacs outputs when there are warnings) and all the molecules seem to hold their places in the crystal, but then at step 9 suddenly some of the molecules become misshapen with very long or very short bonds. Of course it goes downhill from there, but I can't figure out what's causing the problems since it's clearly happening from the very beginning (according to the shake warnings). What other things could I look at to troubleshoot my problem? Not sure, but at least the failure happens fast. Upload all your input files somewhere and I'll take a few minutes to see if I can spot anything. -Justin Thanks for your help, Nathan - Original Message - From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Sent: Thursday, July 9, 2015 7:39:47 AM Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault) On 7/8/15 8:06 PM, Nathan K Houtz wrote: Hello, I deleted the email and can't respond to my last reply directly - sorry! I got this response from Mark Abraham: Hi, Try doing some EM and initial equilibration with no constraints at all, perhaps? Mark I tried commenting out the shake commands, and got a short (5000 step) simulation to run just fine without blowing up. Before, I would get shake warnings from the first few steps and a segmentation fault around step 13 or 14. I would like to be able to simulate with rigid molecules, though. Why would the simulation work with flexible molecules but not rigid ones? Flexible water allows weird geometry, which is probably coming up and causing your constraint algorithm to fail. I'd inspect the outcome carefully. Just because it runs doesn't mean it's right. Also, in the example .mdp file for tip4p water, there is the (outdated) option, 'unconstrained-start', which is now 'continuation'. I got errors when trying to make the input .tpr file when I attempted to set that option to 'yes'. The warning said it was because I want Gromacs to generate velocities to start the simulation, which is incompatible with that command. Is there another way I can try to start the simulation unconstrained? Or would you suggest another idea to fix my shake warnings? What this setting says is have the constraints already been solved (continuation = yes) or should mdrun constrain the starting configuration itself (continuation = no). The .mdp file has a number of weird settings. I would never use Nose-Hoover and Parrinello-Rahman when generating velocities; that's likely to be very unstable. See if a more forgiving thermostat and/or barostat resolves the issue, e.g. tcoupl = v-rescale and pcoupl = Berendsen. Also note that the cutoffs are very short (probably because they want to use a small box, but note that it *does* affect the physics) and nstlist = 1 is totally unnecessary. It doesn't hurt your physics, but it's a major waste of performance. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http
Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault)
Actually, I think I found the problem. When i looked at the pdb files in vmd the first time I missed it, but a colleague had a hunch and I found that he was right! I think that shake is constraining atoms to the wrong molecules. Here's a screenshot I took where you can see what I mean:http://imgur.com/1bgThDv I'm still not sure how to fix it though. The molecule numbering in my .gro file is correct, and there are only 4 atoms per molecule (or 3 plus the dummy). How can I tell shake to look at each molecule individually? Or have I made a mistake somewhere? Here are my most recent files: .gro file: (only part of it -- there is a character limit. this is the first and last ten molecules with the box dimensions at the bottom) http://textuploader.com/e898 topology file: http://textuploader.com/e89g minimization: http://textuploader.com/e8rc .mdp file: http://textuploader.com/e896 log file from a failed simulation: http://textuploader.com/e80y Thanks for your help! If you do still want the full .gro file to run the simulation, I can look for a different file host. Nathan - Original Message - From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Sent: Friday, July 10, 2015 5:06:34 PM Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault) On 7/9/15 9:23 PM, Nathan K Houtz wrote: Thanks for your explanations, Dr. Lemkul. I had already corrected a couple of the things you suggested. Gromacs won't actually let me run with Nose-Hoover and Parrinello-Rahman together (or at least, it gives a warning not to do that and stops). I'd like to run in NVT anyway, so I had set Pcoupl to 'no'. I had also increased the cutoffs and my nstlist is 20. I have now also changed the tcoupl to v-rescale, but unfortunately that alone didn't help. So I'm not sure exactly what I can inspect to find the source of my error. I know that temperature, pressure, and total energy are all warning signs of bad things if they misbehave, but they were all fairly constant throughout the simulation. (This is for the flexible-model simulation:) The starting energy for 1700 water molecules at 120K was -1.08744e+05, and it finished at -1.06047e+05 with no significant variations on any step. Pressure and temperature were also fine. I attempted to look at the results visually in vmd but I might have done something wrong because the .trr file has some error in it and vmd crashes. But the starting geometry after minimization looks fine: none of the molecules were moved out of their position in the crystal. For the constrained molecules, the energy stays about the same (about -1e+5) for the first 8 timesteps and then quickly blows up to +2e15 at step 12 before it obviously fails. I get shake warnings from step 0 though. In vmd, the first 8 steps look reasonable (checking the .pdb files that gromacs outputs when there are warnings) and all the molecules seem to hold their places in the crystal, but then at step 9 suddenly some of the molecules become misshapen with very long or very short bonds. Of course it goes downhill from there, but I can't figure out what's causing the problems since it's clearly happening from the very beginning (according to the shake warnings). What other things could I look at to troubleshoot my problem? Not sure, but at least the failure happens fast. Upload all your input files somewhere and I'll take a few minutes to see if I can spot anything. -Justin Thanks for your help, Nathan - Original Message - From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Sent: Thursday, July 9, 2015 7:39:47 AM Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault) On 7/8/15 8:06 PM, Nathan K Houtz wrote: Hello, I deleted the email and can't respond to my last reply directly - sorry! I got this response from Mark Abraham: Hi, Try doing some EM and initial equilibration with no constraints at all, perhaps? Mark I tried commenting out the shake commands, and got a short (5000 step) simulation to run just fine without blowing up. Before, I would get shake warnings from the first few steps and a segmentation fault around step 13 or 14. I would like to be able to simulate with rigid molecules, though. Why would the simulation work with flexible molecules but not rigid ones? Flexible water allows weird geometry, which is probably coming up and causing your constraint algorithm to fail. I'd inspect the outcome carefully. Just because it runs doesn't mean it's right. Also, in the example .mdp file for tip4p water, there is the (outdated) option, 'unconstrained-start', which is now 'continuation'. I got errors when trying to make the input .tpr file when I attempted to set that option to 'yes'. The warning said it was because I want Gromacs to generate velocities to start
Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault)
Hi, That could only happen if your grompp -c input used a different atom ordering from that implied by your [system] section of your .top. grompp warns about this, but maybe you didn't notice... (Or the structure you loaded into VMD is a mismatch to the trajectory, so its heuristics for guessing where bonds actually are get double-crossed.) Mark On Sat, Jul 11, 2015 at 1:15 AM Nathan K Houtz nho...@purdue.edu wrote: Actually, I think I found the problem. When i looked at the pdb files in vmd the first time I missed it, but a colleague had a hunch and I found that he was right! I think that shake is constraining atoms to the wrong molecules. Here's a screenshot I took where you can see what I mean: http://imgur.com/1bgThDv I'm still not sure how to fix it though. The molecule numbering in my .gro file is correct, and there are only 4 atoms per molecule (or 3 plus the dummy). How can I tell shake to look at each molecule individually? Or have I made a mistake somewhere? Here are my most recent files: .gro file: (only part of it -- there is a character limit. this is the first and last ten molecules with the box dimensions at the bottom) http://textuploader.com/e898 topology file: http://textuploader.com/e89g minimization: http://textuploader.com/e8rc .mdp file: http://textuploader.com/e896 log file from a failed simulation: http://textuploader.com/e80y Thanks for your help! If you do still want the full .gro file to run the simulation, I can look for a different file host. Nathan - Original Message - From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Sent: Friday, July 10, 2015 5:06:34 PM Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault) On 7/9/15 9:23 PM, Nathan K Houtz wrote: Thanks for your explanations, Dr. Lemkul. I had already corrected a couple of the things you suggested. Gromacs won't actually let me run with Nose-Hoover and Parrinello-Rahman together (or at least, it gives a warning not to do that and stops). I'd like to run in NVT anyway, so I had set Pcoupl to 'no'. I had also increased the cutoffs and my nstlist is 20. I have now also changed the tcoupl to v-rescale, but unfortunately that alone didn't help. So I'm not sure exactly what I can inspect to find the source of my error. I know that temperature, pressure, and total energy are all warning signs of bad things if they misbehave, but they were all fairly constant throughout the simulation. (This is for the flexible-model simulation:) The starting energy for 1700 water molecules at 120K was -1.08744e+05, and it finished at -1.06047e+05 with no significant variations on any step. Pressure and temperature were also fine. I attempted to look at the results visually in vmd but I might have done something wrong because the .trr file has some error in it and vmd crashes. But the starting geometry after minimization looks fine: none of the molecules were moved out of their position in the crystal. For the constrained molecules, the energy stays about the same (about -1e+5) for the first 8 timesteps and then quickly blows up to +2e15 at step 12 before it obviously fails. I get shake warnings from step 0 though. In vmd, the first 8 steps look reasonable (checking the .pdb files that gromacs outputs when there are warnings) and all the molecules seem to hold their places in the crystal, but then at step 9 suddenly some of the molecules become misshapen with very long or very short bonds. Of course it goes downhill from there, but I can't figure out what's causing the problems since it's clearly happening from the very beginning (according to the shake warnings). What other things could I look at to troubleshoot my problem? Not sure, but at least the failure happens fast. Upload all your input files somewhere and I'll take a few minutes to see if I can spot anything. -Justin Thanks for your help, Nathan - Original Message - From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Sent: Thursday, July 9, 2015 7:39:47 AM Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault) On 7/8/15 8:06 PM, Nathan K Houtz wrote: Hello, I deleted the email and can't respond to my last reply directly - sorry! I got this response from Mark Abraham: Hi, Try doing some EM and initial equilibration with no constraints at all, perhaps? Mark I tried commenting out the shake commands, and got a short (5000 step) simulation to run just fine without blowing up. Before, I would get shake warnings from the first few steps and a segmentation fault around step 13 or 14. I would like to be able to simulate with rigid molecules, though. Why would the simulation work with flexible molecules but not rigid ones? Flexible water allows weird geometry, which
Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault)
Thanks for your explanations, Dr. Lemkul. I had already corrected a couple of the things you suggested. Gromacs won't actually let me run with Nose-Hoover and Parrinello-Rahman together (or at least, it gives a warning not to do that and stops). I'd like to run in NVT anyway, so I had set Pcoupl to 'no'. I had also increased the cutoffs and my nstlist is 20. I have now also changed the tcoupl to v-rescale, but unfortunately that alone didn't help. So I'm not sure exactly what I can inspect to find the source of my error. I know that temperature, pressure, and total energy are all warning signs of bad things if they misbehave, but they were all fairly constant throughout the simulation. (This is for the flexible-model simulation:) The starting energy for 1700 water molecules at 120K was -1.08744e+05, and it finished at -1.06047e+05 with no significant variations on any step. Pressure and temperature were also fine. I attempted to look at the results visually in vmd but I might have done something wrong because the .trr file has some error in it and vmd crashes. But the starting geometry after minimization looks fine: none of the molecules were moved out of their position in the crystal. For the constrained molecules, the energy stays about the same (about -1e+5) for the first 8 timesteps and then quickly blows up to +2e15 at step 12 before it obviously fails. I get shake warnings from step 0 though. In vmd, the first 8 steps look reasonable (checking the .pdb files that gromacs outputs when there are warnings) and all the molecules seem to hold their places in the crystal, but then at step 9 suddenly some of the molecules become misshapen with very long or very short bonds. Of course it goes downhill from there, but I can't figure out what's causing the problems since it's clearly happening from the very beginning (according to the shake warnings). What other things could I look at to troubleshoot my problem? Thanks for your help, Nathan - Original Message - From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Sent: Thursday, July 9, 2015 7:39:47 AM Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault) On 7/8/15 8:06 PM, Nathan K Houtz wrote: Hello, I deleted the email and can't respond to my last reply directly - sorry! I got this response from Mark Abraham: Hi, Try doing some EM and initial equilibration with no constraints at all, perhaps? Mark I tried commenting out the shake commands, and got a short (5000 step) simulation to run just fine without blowing up. Before, I would get shake warnings from the first few steps and a segmentation fault around step 13 or 14. I would like to be able to simulate with rigid molecules, though. Why would the simulation work with flexible molecules but not rigid ones? Flexible water allows weird geometry, which is probably coming up and causing your constraint algorithm to fail. I'd inspect the outcome carefully. Just because it runs doesn't mean it's right. Also, in the example .mdp file for tip4p water, there is the (outdated) option, 'unconstrained-start', which is now 'continuation'. I got errors when trying to make the input .tpr file when I attempted to set that option to 'yes'. The warning said it was because I want Gromacs to generate velocities to start the simulation, which is incompatible with that command. Is there another way I can try to start the simulation unconstrained? Or would you suggest another idea to fix my shake warnings? What this setting says is have the constraints already been solved (continuation = yes) or should mdrun constrain the starting configuration itself (continuation = no). The .mdp file has a number of weird settings. I would never use Nose-Hoover and Parrinello-Rahman when generating velocities; that's likely to be very unstable. See if a more forgiving thermostat and/or barostat resolves the issue, e.g. tcoupl = v-rescale and pcoupl = Berendsen. Also note that the cutoffs are very short (probably because they want to use a small box, but note that it *does* affect the physics) and nstlist = 1 is totally unnecessary. It doesn't hurt your physics, but it's a major waste of performance. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https
Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault)
Hello, I deleted the email and can't respond to my last reply directly - sorry! I got this response from Mark Abraham: Hi, Try doing some EM and initial equilibration with no constraints at all, perhaps? Mark I tried commenting out the shake commands, and got a short (5000 step) simulation to run just fine without blowing up. Before, I would get shake warnings from the first few steps and a segmentation fault around step 13 or 14. I would like to be able to simulate with rigid molecules, though. Why would the simulation work with flexible molecules but not rigid ones? Also, in the example .mdp file for tip4p water, there is the (outdated) option, 'unconstrained-start', which is now 'continuation'. I got errors when trying to make the input .tpr file when I attempted to set that option to 'yes'. The warning said it was because I want Gromacs to generate velocities to start the simulation, which is incompatible with that command. Is there another way I can try to start the simulation unconstrained? Or would you suggest another idea to fix my shake warnings? Thanks very much for your help, Nathan - Original Message - From: Nathan K Houtz nho...@purdue.edu To: gmx-us...@gromacs.org Sent: Monday, July 6, 2015 9:08:33 PM Subject: trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault) Hello, I'm attempting to simulate ice ih in a triclinic box with a rigid tip4p water model. As the subject says, I get warnings (almost immediately) that shake failed to converge in 1000 steps and then eventually a segmentation fault. Gromacs documentation suggests that this is a result of my simulation blowing up. I tried decreasing the timestep down to 0.0001 ps, lowering the temperature, and minimizing further (down to 100 kJ/mol/nm) but nothing worked. I mostly used modified versions of the files available on this page: http://www.sklogwiki.org/SklogWiki/index.php/GROMACS_files_for_the_TIP4P/2005_model except the .gro file, which is my own. I did comment out the pressure coupling algorithms because I got a note that the barostat was unsuitable for equillibration, but I want NVT anyway. The temperature is 120.0 K and the coulomb type is PME. I've double checked and am satisfied with the interaction parameters in the topology file, so I'm out of ideas on where my mistake migh! t be. Here are the commands and files I used, in case it helps: gmx grompp -f minim.mdp -c water_5100.gro -p water_topol.top -o em.tpr gmx mdrun -v -deffnm em gmx grompp -f water_5100.mdp -c em.gro -p water_topol.top -o water.tpr gmx mdrun -deffnm water Here is the minim.mdp file: http://textuploader.com/iggv The water_topol.top file: http://textuploader.com/igpd And the water_5100.mdp file: http://textuploader.com/igzj You'll notice a slight mistake in the naming convention. There are 1700 molecules in the simulation, but everything is named something like '..._5100', even though tip4p water has a virtual site (making 4 particles). My .gro file does in fact have 6800 atoms, not 5100, I just neglected to rename the files because it's easier. Unfortunately I can't upload the .gro file because it's too big. I realize the problem could be there but I won't attach a large file unless it's specifically requested. Here's a sample: Triclinic Frozen Water Simulation 6800 1WATER OW1 0.261 0.000 0.000 0. 0. 0. 1WATER HW2 0.261 0.000 0.082 0. 0. 0. 1WATER HW3 0.343 -0.000 -0.027 0. 0. 0. 1WATER DW4 0.272 0.000 0.007 0. 0. 0. 2WATER OW5 0.261 0.000 0.736 0. 0. 0. 2WATER HW6 0.261 0.000 0.818 0. 0. 0. 2WATER HW7 0.343 0.000 0.709 0. 0. 0. 2WATER DW8 0.272 0.000 0.743 0. 0. 0. 3WATER OW9 0.261 0.000 1.472 0. 0. 0. 3WATER HW 10 0.261 0.000 1.554 0. 0. 0. 3WATER HW 11 0.343 0.000 1.445 0. 0. 0. 3WATER DW 12 0.272 0.000 1.479 0. 0. 0. 4WATER OW 13 0.261 0.000 2.208 0. 0. 0. 4WATER HW 14 0.261 0.000 2.290 0. 0. 0. 4WATER HW 15 0.343 0.000 2.181 0. 0. 0. 4WATER DW 16 0.272 0.000 2.215 0. 0. 0. 5WATER OW 17 0.261 0.000 2.944 0. 0. 0. 5WATER HW 18 0.261 0.000 3.026 0. 0. 0. 5WATER HW 19 0.343 0.000 2.917 0. 0. 0. 5WATER DW 20 0.272 0.000 2.951 0. 0. 0. 6WATER OW 21 -0.130 0.677 0.000 0. 0. 0. 6WATER HW 22 -0.130 0.677 0.082 0. 0. 0. 6WATER HW 23 -0.048 0.677 -0.027 0. 0. 0. 6WATER DW 24 -0.119 0.677
Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault)
Hi, Try doing some EM and initial equilibration with no constraints at all, perhaps? Mark On Tue, Jul 7, 2015 at 3:09 AM Nathan K Houtz nho...@purdue.edu wrote: Hello, I'm attempting to simulate ice ih in a triclinic box with a rigid tip4p water model. As the subject says, I get warnings (almost immediately) that shake failed to converge in 1000 steps and then eventually a segmentation fault. Gromacs documentation suggests that this is a result of my simulation blowing up. I tried decreasing the timestep down to 0.0001 ps, lowering the temperature, and minimizing further (down to 100 kJ/mol/nm) but nothing worked. I mostly used modified versions of the files available on this page: http://www.sklogwiki.org/SklogWiki/index.php/GROMACS_files_for_the_TIP4P/2005_model except the .gro file, which is my own. I did comment out the pressure coupling algorithms because I got a note that the barostat was unsuitable for equillibration, but I want NVT anyway. The temperature is 120.0 K and the coulomb type is PME. I've double checked and am satisfied with the interaction parameters in the topology file, so I'm out of ideas on where my mistake migh! t be. Here are the commands and files I used, in case it helps: gmx grompp -f minim.mdp -c water_5100.gro -p water_topol.top -o em.tpr gmx mdrun -v -deffnm em gmx grompp -f water_5100.mdp -c em.gro -p water_topol.top -o water.tpr gmx mdrun -deffnm water Here is the minim.mdp file: http://textuploader.com/iggv The water_topol.top file: http://textuploader.com/igpd And the water_5100.mdp file: http://textuploader.com/igzj You'll notice a slight mistake in the naming convention. There are 1700 molecules in the simulation, but everything is named something like '..._5100', even though tip4p water has a virtual site (making 4 particles). My .gro file does in fact have 6800 atoms, not 5100, I just neglected to rename the files because it's easier. Unfortunately I can't upload the .gro file because it's too big. I realize the problem could be there but I won't attach a large file unless it's specifically requested. Here's a sample: Triclinic Frozen Water Simulation 6800 1WATER OW1 0.261 0.000 0.000 0. 0. 0. 1WATER HW2 0.261 0.000 0.082 0. 0. 0. 1WATER HW3 0.343 -0.000 -0.027 0. 0. 0. 1WATER DW4 0.272 0.000 0.007 0. 0. 0. 2WATER OW5 0.261 0.000 0.736 0. 0. 0. 2WATER HW6 0.261 0.000 0.818 0. 0. 0. 2WATER HW7 0.343 0.000 0.709 0. 0. 0. 2WATER DW8 0.272 0.000 0.743 0. 0. 0. 3WATER OW9 0.261 0.000 1.472 0. 0. 0. 3WATER HW 10 0.261 0.000 1.554 0. 0. 0. 3WATER HW 11 0.343 0.000 1.445 0. 0. 0. 3WATER DW 12 0.272 0.000 1.479 0. 0. 0. 4WATER OW 13 0.261 0.000 2.208 0. 0. 0. 4WATER HW 14 0.261 0.000 2.290 0. 0. 0. 4WATER HW 15 0.343 0.000 2.181 0. 0. 0. 4WATER DW 16 0.272 0.000 2.215 0. 0. 0. 5WATER OW 17 0.261 0.000 2.944 0. 0. 0. 5WATER HW 18 0.261 0.000 3.026 0. 0. 0. 5WATER HW 19 0.343 0.000 2.917 0. 0. 0. 5WATER DW 20 0.272 0.000 2.951 0. 0. 0. 6WATER OW 21 -0.130 0.677 0.000 0. 0. 0. 6WATER HW 22 -0.130 0.677 0.082 0. 0. 0. 6WATER HW 23 -0.048 0.677 -0.027 0. 0. 0. 6WATER DW 24 -0.119 0.677 0.007 0. 0. 0. . . . . . . 1696WATER OW 6781 1.825 3.160 0.276 0. 0. 0. 1696WATER HW 6782 1.784 3.232 0.304 0. 0. 0. 1696WATER HW 6783 1.907 3.161 0.304 0. 0. 0. 1696WATER DW 6784 1.830 3.170 0.283 0. 0. 0. 1697WATER OW 6785 1.825 3.160 1.012 0. 0. 0. 1697WATER HW 6786 1.784 3.232 1.040 0. 0. 0. 1697WATER HW 6787 1.907 3.161 1.040 0. 0. 0. 1697WATER DW 6788 1.830 3.170 1.019 0. 0. 0. 1698WATER OW 6789 1.825 3.160 1.748 0. 0. 0. 1698WATER HW 6790 1.784 3.232 1.776 0. 0. 0. 1698WATER HW 6791 1.907 3.161 1.776 0. 0. 0. 1698WATER DW 6792 1.830 3.170 1.755 0. 0. 0. 1699WATER OW 6793 1.825 3.160 2.484 0. 0. 0. 1699WATER HW 6794 1.784 3.232 2.512 0. 0. 0. 1699WATER HW 6795 1.907 3.161 2.512 0. 0. 0. 1699WATER DW 6796 1.830 3.170 2.491 0. 0.
[gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault)
Hello, I'm attempting to simulate ice ih in a triclinic box with a rigid tip4p water model. As the subject says, I get warnings (almost immediately) that shake failed to converge in 1000 steps and then eventually a segmentation fault. Gromacs documentation suggests that this is a result of my simulation blowing up. I tried decreasing the timestep down to 0.0001 ps, lowering the temperature, and minimizing further (down to 100 kJ/mol/nm) but nothing worked. I mostly used modified versions of the files available on this page: http://www.sklogwiki.org/SklogWiki/index.php/GROMACS_files_for_the_TIP4P/2005_model except the .gro file, which is my own. I did comment out the pressure coupling algorithms because I got a note that the barostat was unsuitable for equillibration, but I want NVT anyway. The temperature is 120.0 K and the coulomb type is PME. I've double checked and am satisfied with the interaction parameters in the topology file, so I'm out of ideas on where my mistake migh! t be. Here are the commands and files I used, in case it helps: gmx grompp -f minim.mdp -c water_5100.gro -p water_topol.top -o em.tpr gmx mdrun -v -deffnm em gmx grompp -f water_5100.mdp -c em.gro -p water_topol.top -o water.tpr gmx mdrun -deffnm water Here is the minim.mdp file: http://textuploader.com/iggv The water_topol.top file: http://textuploader.com/igpd And the water_5100.mdp file: http://textuploader.com/igzj You'll notice a slight mistake in the naming convention. There are 1700 molecules in the simulation, but everything is named something like '..._5100', even though tip4p water has a virtual site (making 4 particles). My .gro file does in fact have 6800 atoms, not 5100, I just neglected to rename the files because it's easier. Unfortunately I can't upload the .gro file because it's too big. I realize the problem could be there but I won't attach a large file unless it's specifically requested. Here's a sample: Triclinic Frozen Water Simulation 6800 1WATER OW1 0.261 0.000 0.000 0. 0. 0. 1WATER HW2 0.261 0.000 0.082 0. 0. 0. 1WATER HW3 0.343 -0.000 -0.027 0. 0. 0. 1WATER DW4 0.272 0.000 0.007 0. 0. 0. 2WATER OW5 0.261 0.000 0.736 0. 0. 0. 2WATER HW6 0.261 0.000 0.818 0. 0. 0. 2WATER HW7 0.343 0.000 0.709 0. 0. 0. 2WATER DW8 0.272 0.000 0.743 0. 0. 0. 3WATER OW9 0.261 0.000 1.472 0. 0. 0. 3WATER HW 10 0.261 0.000 1.554 0. 0. 0. 3WATER HW 11 0.343 0.000 1.445 0. 0. 0. 3WATER DW 12 0.272 0.000 1.479 0. 0. 0. 4WATER OW 13 0.261 0.000 2.208 0. 0. 0. 4WATER HW 14 0.261 0.000 2.290 0. 0. 0. 4WATER HW 15 0.343 0.000 2.181 0. 0. 0. 4WATER DW 16 0.272 0.000 2.215 0. 0. 0. 5WATER OW 17 0.261 0.000 2.944 0. 0. 0. 5WATER HW 18 0.261 0.000 3.026 0. 0. 0. 5WATER HW 19 0.343 0.000 2.917 0. 0. 0. 5WATER DW 20 0.272 0.000 2.951 0. 0. 0. 6WATER OW 21 -0.130 0.677 0.000 0. 0. 0. 6WATER HW 22 -0.130 0.677 0.082 0. 0. 0. 6WATER HW 23 -0.048 0.677 -0.027 0. 0. 0. 6WATER DW 24 -0.119 0.677 0.007 0. 0. 0. . . . . . . 1696WATER OW 6781 1.825 3.160 0.276 0. 0. 0. 1696WATER HW 6782 1.784 3.232 0.304 0. 0. 0. 1696WATER HW 6783 1.907 3.161 0.304 0. 0. 0. 1696WATER DW 6784 1.830 3.170 0.283 0. 0. 0. 1697WATER OW 6785 1.825 3.160 1.012 0. 0. 0. 1697WATER HW 6786 1.784 3.232 1.040 0. 0. 0. 1697WATER HW 6787 1.907 3.161 1.040 0. 0. 0. 1697WATER DW 6788 1.830 3.170 1.019 0. 0. 0. 1698WATER OW 6789 1.825 3.160 1.748 0. 0. 0. 1698WATER HW 6790 1.784 3.232 1.776 0. 0. 0. 1698WATER HW 6791 1.907 3.161 1.776 0. 0. 0. 1698WATER DW 6792 1.830 3.170 1.755 0. 0. 0. 1699WATER OW 6793 1.825 3.160 2.484 0. 0. 0. 1699WATER HW 6794 1.784 3.232 2.512 0. 0. 0. 1699WATER HW 6795 1.907 3.161 2.512 0. 0. 0. 1699WATER DW 6796 1.830 3.170 2.491 0. 0. 0. 1700WATER OW 6797 1.825 3.160 3.220 0. 0. 0. 1700WATER HW 6798 1.784 3.232 3.248 0. 0. 0. 1700WATER HW 6799 1.907 3.161 3.248 0. 0. 0. 1700WATER
