Re: [gmx-users] to gro or not to gro
You can put whichever spin you like into what is said, but there is a clear (and unnecessary) fault with the way coordinates are stored in gro files when made from pdb using pdb2gmx. On Sun, Nov 27, 2011 at 12:39 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 27/11/2011 5:07 AM, Igor Druz wrote: On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca wrote 1. why repeat the calculations? If you're talking about simulations then there is no need to repeat them due to this. You will get different answers with the same starting coordinates if you simply change the initial velocities. If you're talking about instantaneous energy calculations then I suppose you might need to redo it, but they should be very quick, right? The calculations must be repeated. You are making irrelevant assumptions without knowing what the calculations are for. You asserted that there should have been a warning without explaining why this loss of precision was material. Chris knew that many uses of pdb2gmx change the atomic configuration considerably, e.g. new hydrogen positions, building termini, etc. so that any change of precision of coordinates is not a big deal, and even less important once a simulation has run afterwards. If you want to engage in constructive dialogue, please explain why the loss of precision was material, in order to clarify the reason for your request for a warning message. If you wish to blow off steam, please do it elsewhere. 2. The .gro files do not carry useless zeroes. you have it backwards... the gro files end up with fewer digits. 0.417 or 4.172. Shall I continue? I know which one I prefer. 3. it's a little annoying to find out that you already knew the answer. Why not state that at the outset? Unless I misunderstand this point, this will mark the end of my comments since holding back information on purpose just wastes people's time. Check my 1st e-mail, please. It is NOT asking for clarification. It is requesting an explicit warning message. There's nothing to warn about. You thought that switching from Angstrom to nanometers was significant somehow, and then assumed that different file formats would definitely contain identical information, and didn't check their contents. Mark Chris. -- original message -- I already knew the reason. But I had to find this out hard way. Now facing a dreading prospect of repeating tons of calculations! Hence the request for the bad for the health sign. Btw, gromacs issues a lot of warnings, but not this one :D What a bright idea to switch from angstroms to nanometers! Now the gro files carry a lot of useless zeros. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] to gro or not to gro
My my. Why is it a fault to adhere to ISO units (nm) over non-standard (A)? It's a choice, but a choice is not faulty. The consequences may be undesirable. But shouldn't a user, certainly a computation scientist, understand the file formats, as an experimentalist should know its solvent? And know the consequences of using one over another? Mark is correct to state that a picometer uncertainty at the start has no consequences for molecular dynamics simulations. For single point eneriges they will have. But no one ever forced anyone to use GRO rather than PDB format. That's the choice the researcher makes. And, at least in my tutorial, that difference between GRO and PDB format is stressed. The choice to use standard units is historical, and lies decades back in time. Could we now change it to A, because a 'faulty' choice was made? I'm terribly sorry that you need to do a lot of work again, Igor. But you can't shove the blame in another's shoes. You overlooked something, lead by presumptions about standardization in units and file formats. May I wonder why you only found out now, after all the work has been done? This difference would have showed up with the first test, right? But again, it's not us against you, and I'm sorry you have to go through this. Trust me, most of us have had such moments, although with a different aspect. Best, Tsjerk On Sun, Nov 27, 2011 at 11:03 AM, Igor Druz idruz...@gmail.com wrote: You can put whichever spin you like into what is said, but there is a clear (and unnecessary) fault with the way coordinates are stored in gro files when made from pdb using pdb2gmx. On Sun, Nov 27, 2011 at 12:39 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 27/11/2011 5:07 AM, Igor Druz wrote: On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca wrote 1. why repeat the calculations? If you're talking about simulations then there is no need to repeat them due to this. You will get different answers with the same starting coordinates if you simply change the initial velocities. If you're talking about instantaneous energy calculations then I suppose you might need to redo it, but they should be very quick, right? The calculations must be repeated. You are making irrelevant assumptions without knowing what the calculations are for. You asserted that there should have been a warning without explaining why this loss of precision was material. Chris knew that many uses of pdb2gmx change the atomic configuration considerably, e.g. new hydrogen positions, building termini, etc. so that any change of precision of coordinates is not a big deal, and even less important once a simulation has run afterwards. If you want to engage in constructive dialogue, please explain why the loss of precision was material, in order to clarify the reason for your request for a warning message. If you wish to blow off steam, please do it elsewhere. 2. The .gro files do not carry useless zeroes. you have it backwards... the gro files end up with fewer digits. 0.417 or 4.172. Shall I continue? I know which one I prefer. 3. it's a little annoying to find out that you already knew the answer. Why not state that at the outset? Unless I misunderstand this point, this will mark the end of my comments since holding back information on purpose just wastes people's time. Check my 1st e-mail, please. It is NOT asking for clarification. It is requesting an explicit warning message. There's nothing to warn about. You thought that switching from Angstrom to nanometers was significant somehow, and then assumed that different file formats would definitely contain identical information, and didn't check their contents. Mark Chris. -- original message -- I already knew the reason. But I had to find this out hard way. Now facing a dreading prospect of repeating tons of calculations! Hence the request for the bad for the health sign. Btw, gromacs issues a lot of warnings, but not this one :D What a bright idea to switch from angstroms to nanometers! Now the gro files carry a lot of useless zeros. -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org
Re: [gmx-users] to gro or not to gro
You are missing the point. Quoting my response to David: I appreciate the history of the matter, but it would save a lot of headache to store coordinates in angstroms in gro files, i.e., not to omit 2 in 4.172 A in the pdb file by converting it to 0.417 nm in the gro file. What is the point in dropping useful 2 by introducing useless 0? On Sun, Nov 27, 2011 at 10:30 AM, Tsjerk Wassenaar tsje...@gmail.comwrote: My my. Why is it a fault to adhere to ISO units (nm) over non-standard (A)? It's a choice, but a choice is not faulty. The consequences may be undesirable. But shouldn't a user, certainly a computation scientist, understand the file formats, as an experimentalist should know its solvent? And know the consequences of using one over another? Mark is correct to state that a picometer uncertainty at the start has no consequences for molecular dynamics simulations. For single point eneriges they will have. But no one ever forced anyone to use GRO rather than PDB format. That's the choice the researcher makes. And, at least in my tutorial, that difference between GRO and PDB format is stressed. The choice to use standard units is historical, and lies decades back in time. Could we now change it to A, because a 'faulty' choice was made? I'm terribly sorry that you need to do a lot of work again, Igor. But you can't shove the blame in another's shoes. You overlooked something, lead by presumptions about standardization in units and file formats. May I wonder why you only found out now, after all the work has been done? This difference would have showed up with the first test, right? But again, it's not us against you, and I'm sorry you have to go through this. Trust me, most of us have had such moments, although with a different aspect. Best, Tsjerk On Sun, Nov 27, 2011 at 11:03 AM, Igor Druz idruz...@gmail.com wrote: You can put whichever spin you like into what is said, but there is a clear (and unnecessary) fault with the way coordinates are stored in gro files when made from pdb using pdb2gmx. On Sun, Nov 27, 2011 at 12:39 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 27/11/2011 5:07 AM, Igor Druz wrote: On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca wrote 1. why repeat the calculations? If you're talking about simulations then there is no need to repeat them due to this. You will get different answers with the same starting coordinates if you simply change the initial velocities. If you're talking about instantaneous energy calculations then I suppose you might need to redo it, but they should be very quick, right? The calculations must be repeated. You are making irrelevant assumptions without knowing what the calculations are for. You asserted that there should have been a warning without explaining why this loss of precision was material. Chris knew that many uses of pdb2gmx change the atomic configuration considerably, e.g. new hydrogen positions, building termini, etc. so that any change of precision of coordinates is not a big deal, and even less important once a simulation has run afterwards. If you want to engage in constructive dialogue, please explain why the loss of precision was material, in order to clarify the reason for your request for a warning message. If you wish to blow off steam, please do it elsewhere. 2. The .gro files do not carry useless zeroes. you have it backwards... the gro files end up with fewer digits. 0.417 or 4.172. Shall I continue? I know which one I prefer. 3. it's a little annoying to find out that you already knew the answer. Why not state that at the outset? Unless I misunderstand this point, this will mark the end of my comments since holding back information on purpose just wastes people's time. Check my 1st e-mail, please. It is NOT asking for clarification. It is requesting an explicit warning message. There's nothing to warn about. You thought that switching from Angstrom to nanometers was significant somehow, and then assumed that different file formats would definitely contain identical information, and didn't check their contents. Mark Chris. -- original message -- I already knew the reason. But I had to find this out hard way. Now facing a dreading prospect of repeating tons of calculations! Hence the request for the bad for the health sign. Btw, gromacs issues a lot of warnings, but not this one :D What a bright idea to switch from angstroms to nanometers! Now the gro files carry a lot of useless zeros. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read
Re: [gmx-users] to gro or not to gro
Hi Igor, Please do read the manual. The GRO file format is a fixed-width format with %8.3f for coordinates, velocities and forces. Changing the format to %9.4f will break everything written in fortran. And, yes, people still use fortran. So which point did I miss? :) Cheers, Tsjerk On Sun, Nov 27, 2011 at 11:38 AM, Igor Druz idruz...@gmail.com wrote: You are missing the point. Quoting my response to David: I appreciate the history of the matter, but it would save a lot of headache to store coordinates in angstroms in gro files, i.e., not to omit 2 in 4.172 A in the pdb file by converting it to 0.417 nm in the gro file. What is the point in dropping useful 2 by introducing useless 0? On Sun, Nov 27, 2011 at 10:30 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: My my. Why is it a fault to adhere to ISO units (nm) over non-standard (A)? It's a choice, but a choice is not faulty. The consequences may be undesirable. But shouldn't a user, certainly a computation scientist, understand the file formats, as an experimentalist should know its solvent? And know the consequences of using one over another? Mark is correct to state that a picometer uncertainty at the start has no consequences for molecular dynamics simulations. For single point eneriges they will have. But no one ever forced anyone to use GRO rather than PDB format. That's the choice the researcher makes. And, at least in my tutorial, that difference between GRO and PDB format is stressed. The choice to use standard units is historical, and lies decades back in time. Could we now change it to A, because a 'faulty' choice was made? I'm terribly sorry that you need to do a lot of work again, Igor. But you can't shove the blame in another's shoes. You overlooked something, lead by presumptions about standardization in units and file formats. May I wonder why you only found out now, after all the work has been done? This difference would have showed up with the first test, right? But again, it's not us against you, and I'm sorry you have to go through this. Trust me, most of us have had such moments, although with a different aspect. Best, Tsjerk On Sun, Nov 27, 2011 at 11:03 AM, Igor Druz idruz...@gmail.com wrote: You can put whichever spin you like into what is said, but there is a clear (and unnecessary) fault with the way coordinates are stored in gro files when made from pdb using pdb2gmx. On Sun, Nov 27, 2011 at 12:39 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 27/11/2011 5:07 AM, Igor Druz wrote: On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca wrote 1. why repeat the calculations? If you're talking about simulations then there is no need to repeat them due to this. You will get different answers with the same starting coordinates if you simply change the initial velocities. If you're talking about instantaneous energy calculations then I suppose you might need to redo it, but they should be very quick, right? The calculations must be repeated. You are making irrelevant assumptions without knowing what the calculations are for. You asserted that there should have been a warning without explaining why this loss of precision was material. Chris knew that many uses of pdb2gmx change the atomic configuration considerably, e.g. new hydrogen positions, building termini, etc. so that any change of precision of coordinates is not a big deal, and even less important once a simulation has run afterwards. If you want to engage in constructive dialogue, please explain why the loss of precision was material, in order to clarify the reason for your request for a warning message. If you wish to blow off steam, please do it elsewhere. 2. The .gro files do not carry useless zeroes. you have it backwards... the gro files end up with fewer digits. 0.417 or 4.172. Shall I continue? I know which one I prefer. 3. it's a little annoying to find out that you already knew the answer. Why not state that at the outset? Unless I misunderstand this point, this will mark the end of my comments since holding back information on purpose just wastes people's time. Check my 1st e-mail, please. It is NOT asking for clarification. It is requesting an explicit warning message. There's nothing to warn about. You thought that switching from Angstrom to nanometers was significant somehow, and then assumed that different file formats would definitely contain identical information, and didn't check their contents. Mark Chris. -- original message -- I already knew the reason. But I had to find this out hard way. Now facing a dreading prospect of repeating tons of calculations! Hence the request for the bad for the health sign. Btw, gromacs issues a lot of warnings, but not this one :D What a bright idea to switch from angstroms to nanometers! Now the gro
Re: [gmx-users] to gro or not to gro
write to gro in angstroms, read from gro in angstroms, convert into nm in grompp. On Sun, Nov 27, 2011 at 10:41 AM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Igor, Please do read the manual. The GRO file format is a fixed-width format with %8.3f for coordinates, velocities and forces. Changing the format to %9.4f will break everything written in fortran. And, yes, people still use fortran. So which point did I miss? :) Cheers, Tsjerk On Sun, Nov 27, 2011 at 11:38 AM, Igor Druz idruz...@gmail.com wrote: You are missing the point. Quoting my response to David: I appreciate the history of the matter, but it would save a lot of headache to store coordinates in angstroms in gro files, i.e., not to omit 2 in 4.172 A in the pdb file by converting it to 0.417 nm in the gro file. What is the point in dropping useful 2 by introducing useless 0? On Sun, Nov 27, 2011 at 10:30 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: My my. Why is it a fault to adhere to ISO units (nm) over non-standard (A)? It's a choice, but a choice is not faulty. The consequences may be undesirable. But shouldn't a user, certainly a computation scientist, understand the file formats, as an experimentalist should know its solvent? And know the consequences of using one over another? Mark is correct to state that a picometer uncertainty at the start has no consequences for molecular dynamics simulations. For single point eneriges they will have. But no one ever forced anyone to use GRO rather than PDB format. That's the choice the researcher makes. And, at least in my tutorial, that difference between GRO and PDB format is stressed. The choice to use standard units is historical, and lies decades back in time. Could we now change it to A, because a 'faulty' choice was made? I'm terribly sorry that you need to do a lot of work again, Igor. But you can't shove the blame in another's shoes. You overlooked something, lead by presumptions about standardization in units and file formats. May I wonder why you only found out now, after all the work has been done? This difference would have showed up with the first test, right? But again, it's not us against you, and I'm sorry you have to go through this. Trust me, most of us have had such moments, although with a different aspect. Best, Tsjerk On Sun, Nov 27, 2011 at 11:03 AM, Igor Druz idruz...@gmail.com wrote: You can put whichever spin you like into what is said, but there is a clear (and unnecessary) fault with the way coordinates are stored in gro files when made from pdb using pdb2gmx. On Sun, Nov 27, 2011 at 12:39 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 27/11/2011 5:07 AM, Igor Druz wrote: On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca wrote 1. why repeat the calculations? If you're talking about simulations then there is no need to repeat them due to this. You will get different answers with the same starting coordinates if you simply change the initial velocities. If you're talking about instantaneous energy calculations then I suppose you might need to redo it, but they should be very quick, right? The calculations must be repeated. You are making irrelevant assumptions without knowing what the calculations are for. You asserted that there should have been a warning without explaining why this loss of precision was material. Chris knew that many uses of pdb2gmx change the atomic configuration considerably, e.g. new hydrogen positions, building termini, etc. so that any change of precision of coordinates is not a big deal, and even less important once a simulation has run afterwards. If you want to engage in constructive dialogue, please explain why the loss of precision was material, in order to clarify the reason for your request for a warning message. If you wish to blow off steam, please do it elsewhere. 2. The .gro files do not carry useless zeroes. you have it backwards... the gro files end up with fewer digits. 0.417 or 4.172. Shall I continue? I know which one I prefer. 3. it's a little annoying to find out that you already knew the answer. Why not state that at the outset? Unless I misunderstand this point, this will mark the end of my comments since holding back information on purpose just wastes people's time. Check my 1st e-mail, please. It is NOT asking for clarification. It is requesting an explicit warning message. There's nothing to warn about. You thought that switching from Angstrom to nanometers was significant somehow, and then assumed that different file formats would definitely contain identical information, and didn't check their contents. Mark Chris. -- original message -- I already knew the reason. But I
Re: [gmx-users] to gro or not to gro
On 2011-11-27 12:15, Igor Druz wrote: write to gro in angstroms, read from gro in angstroms, convert into nm in grompp. once more you don't have to use gro, use g96 if precision is important. if we'd introduce a gro format in angstrom it couldn't be called .gro anyway since that would confuse tons of programs using it. On Sun, Nov 27, 2011 at 10:41 AM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi Igor, Please do read the manual. The GRO file format is a fixed-width format with %8.3f for coordinates, velocities and forces. Changing the format to %9.4f will break everything written in fortran. And, yes, people still use fortran. So which point did I miss? :) Cheers, Tsjerk On Sun, Nov 27, 2011 at 11:38 AM, Igor Druz idruz...@gmail.com mailto:idruz...@gmail.com wrote: You are missing the point. Quoting my response to David: I appreciate the history of the matter, but it would save a lot of headache to store coordinates in angstroms in gro files, i.e., not to omit 2 in 4.172 A in the pdb file by converting it to 0.417 nm in the gro file. What is the point in dropping useful 2 by introducing useless 0? On Sun, Nov 27, 2011 at 10:30 AM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: My my. Why is it a fault to adhere to ISO units (nm) over non-standard (A)? It's a choice, but a choice is not faulty. The consequences may be undesirable. But shouldn't a user, certainly a computation scientist, understand the file formats, as an experimentalist should know its solvent? And know the consequences of using one over another? Mark is correct to state that a picometer uncertainty at the start has no consequences for molecular dynamics simulations. For single point eneriges they will have. But no one ever forced anyone to use GRO rather than PDB format. That's the choice the researcher makes. And, at least in my tutorial, that difference between GRO and PDB format is stressed. The choice to use standard units is historical, and lies decades back in time. Could we now change it to A, because a 'faulty' choice was made? I'm terribly sorry that you need to do a lot of work again, Igor. But you can't shove the blame in another's shoes. You overlooked something, lead by presumptions about standardization in units and file formats. May I wonder why you only found out now, after all the work has been done? This difference would have showed up with the first test, right? But again, it's not us against you, and I'm sorry you have to go through this. Trust me, most of us have had such moments, although with a different aspect. Best, Tsjerk On Sun, Nov 27, 2011 at 11:03 AM, Igor Druz idruz...@gmail.com mailto:idruz...@gmail.com wrote: You can put whichever spin you like into what is said, but there is a clear (and unnecessary) fault with the way coordinates are stored in gro files when made from pdb using pdb2gmx. On Sun, Nov 27, 2011 at 12:39 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 27/11/2011 5:07 AM, Igor Druz wrote: On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca wrote 1. why repeat the calculations? If you're talking about simulations then there is no need to repeat them due to this. You will get different answers with the same starting coordinates if you simply change the initial velocities. If you're talking about instantaneous energy calculations then I suppose you might need to redo it, but they should be very quick, right? The calculations must be repeated. You are making irrelevant assumptions without knowing what the calculations are for. You asserted that there should have been a warning without explaining why this loss of precision was material. Chris knew that many uses of pdb2gmx change the atomic configuration considerably, e.g. new hydrogen positions, building termini, etc. so that any change of precision of coordinates is not a big deal, and even less important once a simulation has run afterwards. If you want to engage in constructive dialogue, please explain why the loss of precision was material, in order to clarify the reason for your request for a warning message. If you wish to blow off steam, please do it elsewhere. 2. The .gro files do not carry useless zeroes. you have it
Re: [gmx-users] to gro or not to gro
On 27/11/2011 10:15 PM, Igor Druz wrote: write to gro in angstroms, read from gro in angstroms, convert into nm in grompp. What are you trying to communicate with this hypothetical workflow? Historical file formats imply particular units and are often limited to a particular precision. Nothing should or will be done to change this. Eventually file formats will be flexible enough to specify arbitrary precision in arbitrary units, but that day is not here yet. Even when we get there, workmen will still have to know about their tools work in order to use them. I still haven't seen any evidence beyond Igor's assertion that there's a problem worth a warning, so I'm going to regard that issue as closed. Mark On Sun, Nov 27, 2011 at 10:41 AM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi Igor, Please do read the manual. The GRO file format is a fixed-width format with %8.3f for coordinates, velocities and forces. Changing the format to %9.4f will break everything written in fortran. And, yes, people still use fortran. So which point did I miss? :) Cheers, Tsjerk On Sun, Nov 27, 2011 at 11:38 AM, Igor Druz idruz...@gmail.com mailto:idruz...@gmail.com wrote: You are missing the point. Quoting my response to David: I appreciate the history of the matter, but it would save a lot of headache to store coordinates in angstroms in gro files, i.e., not to omit 2 in 4.172 A in the pdb file by converting it to 0.417 nm in the gro file. What is the point in dropping useful 2 by introducing useless 0? On Sun, Nov 27, 2011 at 10:30 AM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: My my. Why is it a fault to adhere to ISO units (nm) over non-standard (A)? It's a choice, but a choice is not faulty. The consequences may be undesirable. But shouldn't a user, certainly a computation scientist, understand the file formats, as an experimentalist should know its solvent? And know the consequences of using one over another? Mark is correct to state that a picometer uncertainty at the start has no consequences for molecular dynamics simulations. For single point eneriges they will have. But no one ever forced anyone to use GRO rather than PDB format. That's the choice the researcher makes. And, at least in my tutorial, that difference between GRO and PDB format is stressed. The choice to use standard units is historical, and lies decades back in time. Could we now change it to A, because a 'faulty' choice was made? I'm terribly sorry that you need to do a lot of work again, Igor. But you can't shove the blame in another's shoes. You overlooked something, lead by presumptions about standardization in units and file formats. May I wonder why you only found out now, after all the work has been done? This difference would have showed up with the first test, right? But again, it's not us against you, and I'm sorry you have to go through this. Trust me, most of us have had such moments, although with a different aspect. Best, Tsjerk On Sun, Nov 27, 2011 at 11:03 AM, Igor Druz idruz...@gmail.com mailto:idruz...@gmail.com wrote: You can put whichever spin you like into what is said, but there is a clear (and unnecessary) fault with the way coordinates are stored in gro files when made from pdb using pdb2gmx. On Sun, Nov 27, 2011 at 12:39 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 27/11/2011 5:07 AM, Igor Druz wrote: On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca wrote 1. why repeat the calculations? If you're talking about simulations then there is no need to repeat them due to this. You will get different answers with the same starting coordinates if you simply change the initial velocities. If you're talking about instantaneous energy calculations then I suppose you might need to redo it, but they should be very quick, right? The calculations must be repeated. You are making irrelevant assumptions without knowing what the calculations are for. You asserted that there should have been a warning without explaining why this loss of precision was material. Chris knew that many uses of pdb2gmx change the atomic configuration considerably, e.g. new hydrogen positions, building termini, etc. so that any change of precision of coordinates is not a big deal, and even less important once a simulation has run afterwards. If you want to engage
Re: [gmx-users] to gro or not to gro
On Sun, Nov 27, 2011 at 11:26 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 27/11/2011 10:15 PM, Igor Druz wrote: write to gro in angstroms, read from gro in angstroms, convert into nm in grompp. What are you trying to communicate with this hypothetical workflow? Historical file formats imply particular units and are often limited to a particular precision. Nothing should or will be done to change this. Eventually file formats will be flexible enough to specify arbitrary precision in arbitrary units, but that day is not here yet. Even when we get there, workmen will still have to know about their tools work in order to use them. I still haven't seen any evidence beyond Igor's assertion that there's a problem worth a warning, so I'm going to regard that issue as closed. Mark On Sun, Nov 27, 2011 at 10:41 AM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Igor, Please do read the manual. The GRO file format is a fixed-width format with %8.3f for coordinates, velocities and forces. Changing the format to %9.4f will break everything written in fortran. And, yes, people still use fortran. So which point did I miss? :) Cheers, Tsjerk Back to square one! The point you are missing is that 4.172 A is not equal to 0.417 nm and pdb2gmx does it without any warning. On Sun, Nov 27, 2011 at 11:38 AM, Igor Druz idruz...@gmail.com wrote: You are missing the point. Quoting my response to David: I appreciate the history of the matter, but it would save a lot of headache to store coordinates in angstroms in gro files, i.e., not to omit 2 in 4.172 A in the pdb file by converting it to 0.417 nm in the gro file. What is the point in dropping useful 2 by introducing useless 0? On Sun, Nov 27, 2011 at 10:30 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: My my. Why is it a fault to adhere to ISO units (nm) over non-standard (A)? It's a choice, but a choice is not faulty. The consequences may be undesirable. But shouldn't a user, certainly a computation scientist, understand the file formats, as an experimentalist should know its solvent? And know the consequences of using one over another? Mark is correct to state that a picometer uncertainty at the start has no consequences for molecular dynamics simulations. For single point eneriges they will have. But no one ever forced anyone to use GRO rather than PDB format. That's the choice the researcher makes. And, at least in my tutorial, that difference between GRO and PDB format is stressed. The choice to use standard units is historical, and lies decades back in time. Could we now change it to A, because a 'faulty' choice was made? I'm terribly sorry that you need to do a lot of work again, Igor. But you can't shove the blame in another's shoes. You overlooked something, lead by presumptions about standardization in units and file formats. May I wonder why you only found out now, after all the work has been done? This difference would have showed up with the first test, right? But again, it's not us against you, and I'm sorry you have to go through this. Trust me, most of us have had such moments, although with a different aspect. Best, Tsjerk On Sun, Nov 27, 2011 at 11:03 AM, Igor Druz idruz...@gmail.com wrote: You can put whichever spin you like into what is said, but there is a clear (and unnecessary) fault with the way coordinates are stored in gro files when made from pdb using pdb2gmx. On Sun, Nov 27, 2011 at 12:39 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 27/11/2011 5:07 AM, Igor Druz wrote: On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca wrote 1. why repeat the calculations? If you're talking about simulations then there is no need to repeat them due to this. You will get different answers with the same starting coordinates if you simply change the initial velocities. If you're talking about instantaneous energy calculations then I suppose you might need to redo it, but they should be very quick, right? The calculations must be repeated. You are making irrelevant assumptions without knowing what the calculations are for. You asserted that there should have been a warning without explaining why this loss of precision was material. Chris knew that many uses of pdb2gmx change the atomic configuration considerably, e.g. new hydrogen positions, building termini, etc. so that any change of precision of coordinates is not a big deal, and even less important once a simulation has run afterwards. If you want to engage in constructive dialogue, please explain why the loss of precision was material, in order to clarify the reason for your request for a warning message. If you wish to blow off steam, please do it elsewhere. 2. The .gro files do not carry useless zeroes. you have it backwards... the
Re: [gmx-users] to gro or not to gro
Back to square one! The point you are missing is that 4.172 A is not equal to 0.417 nm and pdb2gmx does it without any warning. You have a point. It is not possible to change the file formats without creating great havoc as I'm sure you understand, but a warning that precision is lost in pdb2gmx, editconf, trjconv is a good idea. We should not make *any* presumptions about what the user wants to do (although it is hard). I've created redmine issue 846 to remind us of this problem. http://redmine.gromacs.org/issues/846 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] to gro or not to gro
There is something not quite right here. I grompp a gro file created from a pdb file using pdb2gmx and run MD to do a single point energy calculation. I then grompp the original pdb file and run MD to do a single point energy calculation. The values of potential energy values are different by about 3 kJ/mol for a small molecule. These things should carry a bad for your health sign :D -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] to gro or not to gro
It's more useful if you provide more information. What was the .pdb file (can I download it from the pdb databank?) was there water? what version of gromacs? was it compiled in double or single precision? what were your mdp parameters? -- original message -- There is something not quite right here. I grompp a gro file created from a pdb file using pdb2gmx and run MD to do a single point energy calculation. I then grompp the original pdb file and run MD to do a single point energy calculation. The values of potential energy values are different by about 3 kJ/mol for a small molecule. These things should carry a bad for your health sign :D -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] to gro or not to gro
There was no water. Version 4.5.5. Single precision. This is what I ran: pdb2gmx -f 1.pdb -p g1 -o g1 grompp -f 1.mdp -c g1.gro -o g1.tpr -p g1.top mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene Potential energy: 1.19780e+02 kJ/mol grompp -f 1.mdp -c 1.pdb -o g1.tpr -p g1.top mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene Potential energy: 1.15997e+02 kJ/mol The mdp file: integrator = md nsteps = 0 nstcomm = 1 nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 1 nstenergy= 1 nstxtcout= 0 nstlist = 0 ns_type = simple pbc = no rlist= 0 rcoulomb = 0 rvdw = 0 gen_vel = no unconstrained-start = yes lincs-warnangle = 30 The pdb file : HETATM1 1HH3 ACE 1 -1.449 0.109 -0.581 H HETATM2 CH3 ACE 1 -2.101 -0.268 0.202 C HETATM3 2HH3 ACE 1 -1.708 0.090 1.151 H HETATM4 3HH3 ACE 1 -2.109 -1.350 0.189 H HETATM5 C ACE 1 -3.491 0.269 0.000 C HETATM6 O ACE 1 -4.453 -0.401 -0.152 O ATOM 7 N GLY 2 -3.601 1.734 0.000 N ATOM 8 H GLY 2 -3.039 2.278 -0.623 H ATOM 9 CA GLY 2 -4.525 2.391 0.903 C ATOM 10 HA1 GLY 2 -5.539 2.051 0.696 H ATOM 11 HA2 GLY 2 -4.263 2.147 1.932 H ATOM 12 C GLY 2 -4.461 3.901 0.720 C ATOM 13 O GLY 2 -3.677 4.400 -0.128 O HETATM 14 N NME 3 -5.316 4.776 1.535 N HETATM 15 H NME 3 -6.182 4.876 1.044 H HETATM 16 CH3 NME 3 -4.685 6.072 1.731 C HETATM 17 1HH3 NME 3 -3.754 5.941 2.272 H HETATM 18 2HH3 NME 3 -5.328 6.697 2.341 H HETATM 19 3HH3 NME 3 -4.465 6.615 0.809 H END *In reply to chris.neale at utoronto.ca:* It's more useful if you provide more information. What was the .pdb file (can I download it from the pdb databank?) was there water? what version of gromacs? was it compiled in double or single precision? what were your mdp parameters? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] to gro or not to gro
On 2011-11-26 16:38, Igor Druz wrote: There was no water. Version 4.5.5. Single precision. This is what I ran: pdb2gmx -f 1.pdb -p g1 -o g1 grompp -f 1.mdp -c g1.gro -o g1.tpr -p g1.top mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene Potential energy: 1.19780e+02 kJ/mol grompp -f 1.mdp -c 1.pdb -o g1.tpr -p g1.top mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene Potential energy: 1.15997e+02 kJ/mol the pdb has more decimal digits, hence you have two different sets of coordinates. If you convert the gro back to pdb and the redo the procedure you should get identical numbers. The mdp file: integrator = md nsteps = 0 nstcomm = 1 nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 1 nstenergy= 1 nstxtcout= 0 nstlist = 0 ns_type = simple pbc = no rlist= 0 rcoulomb = 0 rvdw = 0 gen_vel = no unconstrained-start = yes lincs-warnangle = 30 The pdb file : HETATM1 1HH3 ACE 1 -1.449 0.109 -0.581 H HETATM2 CH3 ACE 1 -2.101 -0.268 0.202 C HETATM3 2HH3 ACE 1 -1.708 0.090 1.151 H HETATM4 3HH3 ACE 1 -2.109 -1.350 0.189 H HETATM5 C ACE 1 -3.491 0.269 0.000 C HETATM6 O ACE 1 -4.453 -0.401 -0.152 O ATOM 7 N GLY 2 -3.601 1.734 0.000 N ATOM 8 H GLY 2 -3.039 2.278 -0.623 H ATOM 9 CA GLY 2 -4.525 2.391 0.903 C ATOM 10 HA1 GLY 2 -5.539 2.051 0.696 H ATOM 11 HA2 GLY 2 -4.263 2.147 1.932 H ATOM 12 C GLY 2 -4.461 3.901 0.720 C ATOM 13 O GLY 2 -3.677 4.400 -0.128 O HETATM 14 N NME 3 -5.316 4.776 1.535 N HETATM 15 H NME 3 -6.182 4.876 1.044 H HETATM 16 CH3 NME 3 -4.685 6.072 1.731 C HETATM 17 1HH3 NME 3 -3.754 5.941 2.272 H HETATM 18 2HH3 NME 3 -5.328 6.697 2.341 H HETATM 19 3HH3 NME 3 -4.465 6.615 0.809 H END *In reply to chris.neale at utoronto.ca http://utoronto.ca:* It's more useful if you provide more information. What was the .pdb file (can I download it from the pdb databank?) was there water? what version of gromacs? was it compiled in double or single precision? what were your mdp parameters? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] to gro or not to gro
There is rounding because of angstroms vs nanometers and both files maintain 3 decimal places (see below). The intention of pdb2gmx is not to get a .gro , but to get a .top or .itp file. I see your point, but I don't think it matters. If you really need that precision, then I'd think that you'd be using double precision gromacs (which would still round the output .gro from pdb2gmx and not solve this issue... just saying). gpc-f101n084-$ tail a.gro 2GLYHA2 11 -0.426 0.215 0.193 2GLY C 12 -0.446 0.390 0.072 2GLY O 13 -0.368 0.440 -0.013 3NME N 14 -0.532 0.478 0.154 3NME H 15 -0.618 0.488 0.104 3NMECH3 16 -0.468 0.607 0.173 3NME HH31 17 -0.375 0.594 0.227 3NME HH32 18 -0.533 0.670 0.234 3NME HH33 19 -0.447 0.661 0.081 0.47330 0.80470 0.29640 gpc-f101n084-$ tail a.pdb ATOM 11 HA2 GLY 2 -4.263 2.147 1.932 ATOM 12 C GLY 2 -4.461 3.901 0.720 ATOM 13 O GLY 2 -3.677 4.400 -0.128 HETATM 14 N NME 3 -5.316 4.776 1.535 HETATM 15 H NME 3 -6.182 4.876 1.044 HETATM 16 CH3 NME 3 -4.685 6.072 1.731 HETATM 17 1HH3 NME 3 -3.754 5.941 2.272 HETATM 18 2HH3 NME 3 -5.328 6.697 2.341 HETATM 19 3HH3 NME 3 -4.465 6.615 0.809 END -- original message -- There was no water. Version 4.5.5. Single precision. This is what I ran: pdb2gmx -f 1.pdb -p g1 -o g1 grompp -f 1.mdp -c g1.gro -o g1.tpr -p g1.top mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene Potential energy: 1.19780e+02 kJ/mol grompp -f 1.mdp -c 1.pdb -o g1.tpr -p g1.top mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene Potential energy: 1.15997e+02 kJ/mol The mdp file: integrator = md nsteps = 0 nstcomm = 1 nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 1 nstenergy= 1 nstxtcout= 0 nstlist = 0 ns_type = simple pbc = no rlist= 0 rcoulomb = 0 rvdw = 0 gen_vel = no unconstrained-start = yes lincs-warnangle = 30 The pdb file : HETATM1 1HH3 ACE 1 -1.449 0.109 -0.581 H HETATM2 CH3 ACE 1 -2.101 -0.268 0.202 C HETATM3 2HH3 ACE 1 -1.708 0.090 1.151 H HETATM4 3HH3 ACE 1 -2.109 -1.350 0.189 H HETATM5 C ACE 1 -3.491 0.269 0.000 C HETATM6 O ACE 1 -4.453 -0.401 -0.152 O ATOM 7 N GLY 2 -3.601 1.734 0.000 N ATOM 8 H GLY 2 -3.039 2.278 -0.623 H ATOM 9 CA GLY 2 -4.525 2.391 0.903 C ATOM 10 HA1 GLY 2 -5.539 2.051 0.696 H ATOM 11 HA2 GLY 2 -4.263 2.147 1.932 H ATOM 12 C GLY 2 -4.461 3.901 0.720 C ATOM 13 O GLY 2 -3.677 4.400 -0.128 O HETATM 14 N NME 3 -5.316 4.776 1.535 N HETATM 15 H NME 3 -6.182 4.876 1.044 H HETATM 16 CH3 NME 3 -4.685 6.072 1.731 C HETATM 17 1HH3 NME 3 -3.754 5.941 2.272 H HETATM 18 2HH3 NME 3 -5.328 6.697 2.341 H HETATM 19 3HH3 NME 3 -4.465 6.615 0.809 H END *In reply to chris.neale at utoronto.ca:* It's more useful if you provide more information. What was the .pdb file (can I download it from the pdb databank?) was there water? what version of gromacs? was it compiled in double or single precision? what were your mdp parameters? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] to gro or not to gro
I already knew the reason. But I had to find this out hard way. Now facing a dreading prospect of repeating tons of calculations! Hence the request for the bad for the health sign. Btw, gromacs issues a lot of warnings, but not this one :D What a bright idea to switch from angstroms to nanometers! Now the gro files carry a lot of useless zeros. On Sat, Nov 26, 2011 at 3:55 PM, chris.ne...@utoronto.ca wrote: There is rounding because of angstroms vs nanometers and both files maintain 3 decimal places (see below). The intention of pdb2gmx is not to get a .gro , but to get a .top or .itp file. I see your point, but I don't think it matters. If you really need that precision, then I'd think that you'd be using double precision gromacs (which would still round the output .gro from pdb2gmx and not solve this issue... just saying). gpc-f101n084-$ tail a.gro 2GLYHA2 11 -0.426 0.215 0.193 2GLY C 12 -0.446 0.390 0.072 2GLY O 13 -0.368 0.440 -0.013 3NME N 14 -0.532 0.478 0.154 3NME H 15 -0.618 0.488 0.104 3NMECH3 16 -0.468 0.607 0.173 3NME HH31 17 -0.375 0.594 0.227 3NME HH32 18 -0.533 0.670 0.234 3NME HH33 19 -0.447 0.661 0.081 0.47330 0.80470 0.29640 gpc-f101n084-$ tail a.pdb ATOM 11 HA2 GLY 2 -4.263 2.147 1.932 ATOM 12 C GLY 2 -4.461 3.901 0.720 ATOM 13 O GLY 2 -3.677 4.400 -0.128 HETATM 14 N NME 3 -5.316 4.776 1.535 HETATM 15 H NME 3 -6.182 4.876 1.044 HETATM 16 CH3 NME 3 -4.685 6.072 1.731 HETATM 17 1HH3 NME 3 -3.754 5.941 2.272 HETATM 18 2HH3 NME 3 -5.328 6.697 2.341 HETATM 19 3HH3 NME 3 -4.465 6.615 0.809 END -- original message -- There was no water. Version 4.5.5. Single precision. This is what I ran: pdb2gmx -f 1.pdb -p g1 -o g1 grompp -f 1.mdp -c g1.gro -o g1.tpr -p g1.top mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene Potential energy: 1.19780e+02 kJ/mol grompp -f 1.mdp -c 1.pdb -o g1.tpr -p g1.top mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene Potential energy: 1.15997e+02 kJ/mol The mdp file: integrator = md nsteps = 0 nstcomm = 1 nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 1 nstenergy= 1 nstxtcout= 0 nstlist = 0 ns_type = simple pbc = no rlist= 0 rcoulomb = 0 rvdw = 0 gen_vel = no unconstrained-start = yes lincs-warnangle = 30 The pdb file : HETATM1 1HH3 ACE 1 -1.449 0.109 -0.581 H HETATM2 CH3 ACE 1 -2.101 -0.268 0.202 C HETATM3 2HH3 ACE 1 -1.708 0.090 1.151 H HETATM4 3HH3 ACE 1 -2.109 -1.350 0.189 H HETATM5 C ACE 1 -3.491 0.269 0.000 C HETATM6 O ACE 1 -4.453 -0.401 -0.152 O ATOM 7 N GLY 2 -3.601 1.734 0.000 N ATOM 8 H GLY 2 -3.039 2.278 -0.623 H ATOM 9 CA GLY 2 -4.525 2.391 0.903 C ATOM 10 HA1 GLY 2 -5.539 2.051 0.696 H ATOM 11 HA2 GLY 2 -4.263 2.147 1.932 H ATOM 12 C GLY 2 -4.461 3.901 0.720 C ATOM 13 O GLY 2 -3.677 4.400 -0.128 O HETATM 14 N NME 3 -5.316 4.776 1.535 N HETATM 15 H NME 3 -6.182 4.876 1.044 H HETATM 16 CH3 NME 3 -4.685 6.072 1.731 C HETATM 17 1HH3 NME 3 -3.754 5.941 2.272 H HETATM 18 2HH3 NME 3 -5.328 6.697 2.341 H HETATM 19 3HH3 NME 3 -4.465 6.615 0.809 H END *In reply to chris.neale at utoronto.ca:* It's more useful if you provide more information. What was the .pdb file (can I download it from the pdb databank?) was there water? what version of gromacs? was it compiled in double or single precision? what were your mdp parameters? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
[gmx-users] to gro or not to gro
1. why repeat the calculations? If you're talking about simulations then there is no need to repeat them due to this. You will get different answers with the same starting coordinates if you simply change the initial velocities. If you're talking about instantaneous energy calculations then I suppose you might need to redo it, but they should be very quick, right? 2. The .gro files do not carry useless zeroes. you have it backwards... the gro files end up with fewer digits. 3. it's a little annoying to find out that you already knew the answer. Why not state that at the outset? Unless I misunderstand this point, this will mark the end of my comments since holding back information on purpose just wastes people's time. Chris. -- original message -- I already knew the reason. But I had to find this out hard way. Now facing a dreading prospect of repeating tons of calculations! Hence the request for the bad for the health sign. Btw, gromacs issues a lot of warnings, but not this one :D What a bright idea to switch from angstroms to nanometers! Now the gro files carry a lot of useless zeros. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] to gro or not to gro
On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca wrote 1. why repeat the calculations? If you're talking about simulations then there is no need to repeat them due to this. You will get different answers with the same starting coordinates if you simply change the initial velocities. If you're talking about instantaneous energy calculations then I suppose you might need to redo it, but they should be very quick, right? The calculations must be repeated. You are making irrelevant assumptions without knowing what the calculations are for. 2. The .gro files do not carry useless zeroes. you have it backwards... the gro files end up with fewer digits. 0.417 or 4.172. Shall I continue? I know which one I prefer. 3. it's a little annoying to find out that you already knew the answer. Why not state that at the outset? Unless I misunderstand this point, this will mark the end of my comments since holding back information on purpose just wastes people's time. Check my 1st e-mail, please. It is NOT asking for clarification. It is requesting an explicit warning message. Chris. -- original message -- I already knew the reason. But I had to find this out hard way. Now facing a dreading prospect of repeating tons of calculations! Hence the request for the bad for the health sign. Btw, gromacs issues a lot of warnings, but not this one :D What a bright idea to switch from angstroms to nanometers! Now the gro files carry a lot of useless zeros. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] to gro or not to gro
On 2011-11-26 19:07, Igor Druz wrote: On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca wrote 1. why repeat the calculations? If you're talking about simulations then there is no need to repeat them due to this. You will get different answers with the same starting coordinates if you simply change the initial velocities. If you're talking about instantaneous energy calculations then I suppose you might need to redo it, but they should be very quick, right? The calculations must be repeated. You are making irrelevant assumptions without knowing what the calculations are for. 2. The .gro files do not carry useless zeroes. you have it backwards... the gro files end up with fewer digits. 0.417 or 4.172. Shall I continue? I know which one I prefer. 3. it's a little annoying to find out that you already knew the answer. Why not state that at the outset? Unless I misunderstand this point, this will mark the end of my comments since holding back information on purpose just wastes people's time. Check my 1st e-mail, please. It is NOT asking for clarification. It is requesting an explicit warning message. You have the option to use pdb or gro or g96. The last format has even more digits, and support for velocities. Pdb has no velocities and gro has lowest precision. All of these are file formats that have not been developed by the gromacs team, but were adopted from other packages. I don't see what kind of warning we should issue when using a gro file, without making it even more confusing. Chris. -- original message -- I already knew the reason. But I had to find this out hard way. Now facing a dreading prospect of repeating tons of calculations! Hence the request for the bad for the health sign. Btw, gromacs issues a lot of warnings, but not this one :D What a bright idea to switch from angstroms to nanometers! Now the gro files carry a lot of useless zeros. -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] to gro or not to gro
On Sat, Nov 26, 2011 at 6:37 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2011-11-26 19:07, Igor Druz wrote: On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca mailto:chris.neale@utoronto.**ca chris.ne...@utoronto.ca wrote 1. why repeat the calculations? If you're talking about simulations then there is no need to repeat them due to this. You will get different answers with the same starting coordinates if you simply change the initial velocities. If you're talking about instantaneous energy calculations then I suppose you might need to redo it, but they should be very quick, right? The calculations must be repeated. You are making irrelevant assumptions without knowing what the calculations are for. 2. The .gro files do not carry useless zeroes. you have it backwards... the gro files end up with fewer digits. 0.417 or 4.172. Shall I continue? I know which one I prefer. 3. it's a little annoying to find out that you already knew the answer. Why not state that at the outset? Unless I misunderstand this point, this will mark the end of my comments since holding back information on purpose just wastes people's time. Check my 1st e-mail, please. It is NOT asking for clarification. It is requesting an explicit warning message. You have the option to use pdb or gro or g96. The last format has even more digits, and support for velocities. Pdb has no velocities and gro has lowest precision. All of these are file formats that have not been developed by the gromacs team, but were adopted from other packages. I don't see what kind of warning we should issue when using a gro file, without making it even more confusing. it was already in your 1st response: the gro has less decimal digits than pdb when storing coordinates. This should be issued by pdb2gmx. I appreciate the history of the matter, but it would save a lot of headache to store coordinates in angstroms in gro files, i.e., not to omit 2 in 4.172 A in the pdb file by converting it to 0.417 nm in the gro file. What is the point in dropping useful 2 by introducing useless 0? Chris. -- original message -- I already knew the reason. But I had to find this out hard way. Now facing a dreading prospect of repeating tons of calculations! Hence the request for the bad for the health sign. Btw, gromacs issues a lot of warnings, but not this one :D What a bright idea to switch from angstroms to nanometers! Now the gro files carry a lot of useless zeros. -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] to gro or not to gro
On 2011-11-26 20:15, Igor Druz wrote: On Sat, Nov 26, 2011 at 6:37 PM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-11-26 19:07, Igor Druz wrote: On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca mailto:chris.neale@utoronto.__ca mailto:chris.ne...@utoronto.ca wrote 1. why repeat the calculations? If you're talking about simulations then there is no need to repeat them due to this. You will get different answers with the same starting coordinates if you simply change the initial velocities. If you're talking about instantaneous energy calculations then I suppose you might need to redo it, but they should be very quick, right? The calculations must be repeated. You are making irrelevant assumptions without knowing what the calculations are for. 2. The .gro files do not carry useless zeroes. you have it backwards... the gro files end up with fewer digits. 0.417 or 4.172. Shall I continue? I know which one I prefer. 3. it's a little annoying to find out that you already knew the answer. Why not state that at the outset? Unless I misunderstand this point, this will mark the end of my comments since holding back information on purpose just wastes people's time. Check my 1st e-mail, please. It is NOT asking for clarification. It is requesting an explicit warning message. You have the option to use pdb or gro or g96. The last format has even more digits, and support for velocities. Pdb has no velocities and gro has lowest precision. All of these are file formats that have not been developed by the gromacs team, but were adopted from other packages. I don't see what kind of warning we should issue when using a gro file, without making it even more confusing. it was already in your 1st response: the gro has less decimal digits than pdb when storing coordinates. This should be issued by pdb2gmx. I appreciate the history of the matter, but it would save a lot of headache to store coordinates in angstroms in gro files, i.e., not to omit 2 in 4.172 A in the pdb file by converting it to 0.417 nm in the gro file. What is the point in dropping useful 2 by introducing useless 0? History as well. You can have pdb2gmx go straight to g96 (-c conf.g96 will do it) which has higher precision than either of the two others. It is bigger though. As said g96 is also a borrowed format from gromos96. Chris. -- original message -- I already knew the reason. But I had to find this out hard way. Now facing a dreading prospect of repeating tons of calculations! Hence the request for the bad for the health sign. Btw, gromacs issues a lot of warnings, but not this one :D What a bright idea to switch from angstroms to nanometers! Now the gro files carry a lot of useless zeros. -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-request@__gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205 tel:%2B46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users
Re: [gmx-users] to gro or not to gro
On 27/11/2011 5:07 AM, Igor Druz wrote: On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca wrote 1. why repeat the calculations? If you're talking about simulations then there is no need to repeat them due to this. You will get different answers with the same starting coordinates if you simply change the initial velocities. If you're talking about instantaneous energy calculations then I suppose you might need to redo it, but they should be very quick, right? The calculations must be repeated. You are making irrelevant assumptions without knowing what the calculations are for. You asserted that there should have been a warning without explaining why this loss of precision was material. Chris knew that many uses of pdb2gmx change the atomic configuration considerably, e.g. new hydrogen positions, building termini, etc. so that any change of precision of coordinates is not a big deal, and even less important once a simulation has run afterwards. If you want to engage in constructive dialogue, please explain why the loss of precision was material, in order to clarify the reason for your request for a warning message. If you wish to blow off steam, please do it elsewhere. 2. The .gro files do not carry useless zeroes. you have it backwards... the gro files end up with fewer digits. 0.417 or 4.172. Shall I continue? I know which one I prefer. 3. it's a little annoying to find out that you already knew the answer. Why not state that at the outset? Unless I misunderstand this point, this will mark the end of my comments since holding back information on purpose just wastes people's time. Check my 1st e-mail, please. It is NOT asking for clarification. It is requesting an explicit warning message. There's nothing to warn about. You thought that switching from Angstrom to nanometers was significant somehow, and then assumed that different file formats would definitely contain identical information, and didn't check their contents. Mark Chris. -- original message -- I already knew the reason. But I had to find this out hard way. Now facing a dreading prospect of repeating tons of calculations! Hence the request for the bad for the health sign. Btw, gromacs issues a lot of warnings, but not this one :D What a bright idea to switch from angstroms to nanometers! Now the gro files carry a lot of useless zeros. -- gmx-users mailing list gmx-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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
