Re: [gmx-users] trjorder not working
Thanks Justin, that was helpful. I have a following question. Since in my system I have both methanol and water and I want to order both of them ( my eventual aim to make a sphere), is there is way to override -na option ( for water na 4, methanol 3). Is there is way that all the components of the system get ordered with respect to the protein? or I have have to play around ordering them one by one? Thanks, SN On Thu, May 5, 2011 at 4:37 PM, Justin A. Lemkul jalem...@vt.edu wrote: shivangi nangia wrote: Hello, Came back to the set of calculations I was doing few days back. I have a box of water (TIP4P), methanol, protein and DHB anions. I minimized this system. Trying to use trjorder for water molecules with respect to the protein (eventually I want to make a sphere by ordering and getting rid of the molecules I do not want) In the index.ndx file i specified atom 144 (belongs to protein) so when I run trjorder -f em.gro -s em.tpr -n index.ndx -na 4 -o ordered.gro I pick number associated with atom 144 and SOL ( tip4p water) and I generate ordered.gro The sequence for SOL changes ( random), but when I use g_dist as I go down the ordered.gro, there is still no trend ( ascending with respect to protein) I suspect your index file is wrong. Presumably, you have measured distances to individual water molecules using g_dist, which would require a custom index group for each water molecule analyzed, correct? If you use ordered.gro, the residue numbers will indeed be scrambled based on ordering, but the distance will correspond to the original distance, not the ordered one. The solution is to use your unordered coordinate file or .tpr file to create the index group, then perform the distance measurements. Alternatively, use genconf to renumber ordered.gro to get sequential residue numbers, then create whatever index file you might need from the renumbered coordinate file. Also, -da 0 refers to an atom OR COM of the molecule. using trjorder -f em.gro -s em.tpr -n index.ndx -da 0 -na 4 -o ordered.gro and running it and choosing 1 for protein and 14 for SOL means that gromacs automatically understands that protein's COM is to be used to order SOL (tip4p, -na 4) ?? As the documentation is written, yes. If so, then tha talso generates a .gro file which produces random water molecules but there is again no trend. Same problem as above, I suspect. -Justin I am very confused about using trjorder, it will be really helpful if someone or Mark can help me understand. Thanks a lot SN On Thu, Apr 28, 2011 at 9:43 PM, Mark Abraham mark.abra...@anu.edu.aumailto: mark.abra...@anu.edu.au wrote: On 4/29/2011 11:29 AM, shivangi nangia wrote: Hello, The manual explaining trjorder says: trjorder orders molecules according to the smallest distance to atoms in a reference group or on z-coordinate (with option -z). With distance ordering, it will ask for a group of reference atoms and a group of molecules. For each frame of the trajectory the selected molecules will be reordered according to the shortest distance between atom number -da in the molecule and all the atoms in the reference group. *The center of mass of the molecules can be used instead of a reference atom by setting -da to 0* In order to arrange water molecules in accordance with the COM of the polypeptide, I chose -da 0. As it says above, -da refers to an atom or COM of the molecule, not the reference group. This could be worded better in the documentation. Be sure you're choosing the groups you think you are choosing - you not copying relevant parts of your terminal output into emails is making things difficult. Mark Am I wrong? Thanks, SN On Thu, Apr 28, 2011 at 8:29 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 4/29/2011 4:08 AM, shivangi nangia wrote: Hello all, I am trying to order the TIP4P water molecules in my system with respect to the polypeptide in my system. The command I am using is: trjorder -f shape.gro -s shape.tpr -da 0 -na 4 -o ordered.gro This runs without any error and ordered.gro is generated with random sequence of water molecules. Just to cross check I calculated the distances between one of atoms of the polypeptide and oxyegn atom of different ordered water molecules. I found, there is no ascendig trend in the distances with respect to the polypeptide as a go down in the ordered.gro file. What could be going wrong? -da 0 has a particular effect - is it appropriate? Did you choose the right groups? You could use the -nshell option to probe what trjorder thinks is going on. Mark
Re: [gmx-users] trjorder not working
shivangi nangia wrote: Thanks Justin, that was helpful. I have a following question. Since in my system I have both methanol and water and I want to order both of them ( my eventual aim to make a sphere), is there is way to override -na option ( for water na 4, methanol 3). Is there is way that all the components of the system get ordered with respect to the protein? If they all have different numbers of atoms, no. or I have have to play around ordering them one by one? Probably. If your goal is to set up a spherical system, there are probably far easier ways to do this with genbox -shell and/or VMD/NAMD solvation procedures to build spheres. -Justin Thanks, SN On Thu, May 5, 2011 at 4:37 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: shivangi nangia wrote: Hello, Came back to the set of calculations I was doing few days back. I have a box of water (TIP4P), methanol, protein and DHB anions. I minimized this system. Trying to use trjorder for water molecules with respect to the protein (eventually I want to make a sphere by ordering and getting rid of the molecules I do not want) In the index.ndx file i specified atom 144 (belongs to protein) so when I run trjorder -f em.gro -s em.tpr -n index.ndx -na 4 -o ordered.gro I pick number associated with atom 144 and SOL ( tip4p water) and I generate ordered.gro The sequence for SOL changes ( random), but when I use g_dist as I go down the ordered.gro, there is still no trend ( ascending with respect to protein) I suspect your index file is wrong. Presumably, you have measured distances to individual water molecules using g_dist, which would require a custom index group for each water molecule analyzed, correct? If you use ordered.gro, the residue numbers will indeed be scrambled based on ordering, but the distance will correspond to the original distance, not the ordered one. The solution is to use your unordered coordinate file or .tpr file to create the index group, then perform the distance measurements. Alternatively, use genconf to renumber ordered.gro to get sequential residue numbers, then create whatever index file you might need from the renumbered coordinate file. Also, -da 0 refers to an atom OR COM of the molecule. using trjorder -f em.gro -s em.tpr -n index.ndx -da 0 -na 4 -o ordered.gro and running it and choosing 1 for protein and 14 for SOL means that gromacs automatically understands that protein's COM is to be used to order SOL (tip4p, -na 4) ?? As the documentation is written, yes. If so, then tha talso generates a .gro file which produces random water molecules but there is again no trend. Same problem as above, I suspect. -Justin I am very confused about using trjorder, it will be really helpful if someone or Mark can help me understand. Thanks a lot SN On Thu, Apr 28, 2011 at 9:43 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 4/29/2011 11:29 AM, shivangi nangia wrote: Hello, The manual explaining trjorder says: trjorder orders molecules according to the smallest distance to atoms in a reference group or on z-coordinate (with option -z). With distance ordering, it will ask for a group of reference atoms and a group of molecules. For each frame of the trajectory the selected molecules will be reordered according to the shortest distance between atom number -da in the molecule and all the atoms in the reference group. *The center of mass of the molecules can be used instead of a reference atom by setting -da to 0* In order to arrange water molecules in accordance with the COM of the polypeptide, I chose -da 0. As it says above, -da refers to an atom or COM of the molecule, not the reference group. This could be worded better in the documentation. Be sure you're choosing the groups you think you are choosing - you not copying relevant parts of your terminal output into emails is making things difficult. Mark Am I wrong? Thanks, SN On Thu, Apr 28, 2011 at 8:29 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au
Re: [gmx-users] trjorder not working
Hello, Came back to the set of calculations I was doing few days back. I have a box of water (TIP4P), methanol, protein and DHB anions. I minimized this system. Trying to use trjorder for water molecules with respect to the protein (eventually I want to make a sphere by ordering and getting rid of the molecules I do not want) In the index.ndx file i specified atom 144 (belongs to protein) so when I run trjorder -f em.gro -s em.tpr -n index.ndx -na 4 -o ordered.gro I pick number associated with atom 144 and SOL ( tip4p water) and I generate ordered.gro The sequence for SOL changes ( random), but when I use g_dist as I go down the ordered.gro, there is still no trend ( ascending with respect to protein) Also, -da 0 refers to an atom OR COM of the molecule. using trjorder -f em.gro -s em.tpr -n index.ndx -da 0 -na 4 -o ordered.gro and running it and choosing 1 for protein and 14 for SOL means that gromacs automatically understands that protein's COM is to be used to order SOL (tip4p, -na 4) ?? If so, then tha talso generates a .gro file which produces random water molecules but there is again no trend. I am very confused about using trjorder, it will be really helpful if someone or Mark can help me understand. Thanks a lot SN On Thu, Apr 28, 2011 at 9:43 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/29/2011 11:29 AM, shivangi nangia wrote: Hello, The manual explaining trjorder says: trjorder orders molecules according to the smallest distance to atoms in a reference group or on z-coordinate (with option -z). With distance ordering, it will ask for a group of reference atoms and a group of molecules. For each frame of the trajectory the selected molecules will be reordered according to the shortest distance between atom number -da in the molecule and all the atoms in the reference group. *The center of mass of the molecules can be used instead of a reference atom by setting -da to 0* In order to arrange water molecules in accordance with the COM of the polypeptide, I chose -da 0. As it says above, -da refers to an atom or COM of the molecule, not the reference group. This could be worded better in the documentation. Be sure you're choosing the groups you think you are choosing - you not copying relevant parts of your terminal output into emails is making things difficult. Mark Am I wrong? Thanks, SN On Thu, Apr 28, 2011 at 8:29 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/29/2011 4:08 AM, shivangi nangia wrote: Hello all, I am trying to order the TIP4P water molecules in my system with respect to the polypeptide in my system. The command I am using is: trjorder -f shape.gro -s shape.tpr -da 0 -na 4 -o ordered.gro This runs without any error and ordered.gro is generated with random sequence of water molecules. Just to cross check I calculated the distances between one of atoms of the polypeptide and oxyegn atom of different ordered water molecules. I found, there is no ascendig trend in the distances with respect to the polypeptide as a go down in the ordered.gro file. What could be going wrong? -da 0 has a particular effect - is it appropriate? Did you choose the right groups? You could use the -nshell option to probe what trjorder thinks is going on. Mark -- 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 -- 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] trjorder not working
shivangi nangia wrote: Hello, Came back to the set of calculations I was doing few days back. I have a box of water (TIP4P), methanol, protein and DHB anions. I minimized this system. Trying to use trjorder for water molecules with respect to the protein (eventually I want to make a sphere by ordering and getting rid of the molecules I do not want) In the index.ndx file i specified atom 144 (belongs to protein) so when I run trjorder -f em.gro -s em.tpr -n index.ndx -na 4 -o ordered.gro I pick number associated with atom 144 and SOL ( tip4p water) and I generate ordered.gro The sequence for SOL changes ( random), but when I use g_dist as I go down the ordered.gro, there is still no trend ( ascending with respect to protein) I suspect your index file is wrong. Presumably, you have measured distances to individual water molecules using g_dist, which would require a custom index group for each water molecule analyzed, correct? If you use ordered.gro, the residue numbers will indeed be scrambled based on ordering, but the distance will correspond to the original distance, not the ordered one. The solution is to use your unordered coordinate file or .tpr file to create the index group, then perform the distance measurements. Alternatively, use genconf to renumber ordered.gro to get sequential residue numbers, then create whatever index file you might need from the renumbered coordinate file. Also, -da 0 refers to an atom OR COM of the molecule. using trjorder -f em.gro -s em.tpr -n index.ndx -da 0 -na 4 -o ordered.gro and running it and choosing 1 for protein and 14 for SOL means that gromacs automatically understands that protein's COM is to be used to order SOL (tip4p, -na 4) ?? As the documentation is written, yes. If so, then tha talso generates a .gro file which produces random water molecules but there is again no trend. Same problem as above, I suspect. -Justin I am very confused about using trjorder, it will be really helpful if someone or Mark can help me understand. Thanks a lot SN On Thu, Apr 28, 2011 at 9:43 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 4/29/2011 11:29 AM, shivangi nangia wrote: Hello, The manual explaining trjorder says: trjorder orders molecules according to the smallest distance to atoms in a reference group or on z-coordinate (with option -z). With distance ordering, it will ask for a group of reference atoms and a group of molecules. For each frame of the trajectory the selected molecules will be reordered according to the shortest distance between atom number -da in the molecule and all the atoms in the reference group. *The center of mass of the molecules can be used instead of a reference atom by setting -da to 0* In order to arrange water molecules in accordance with the COM of the polypeptide, I chose -da 0. As it says above, -da refers to an atom or COM of the molecule, not the reference group. This could be worded better in the documentation. Be sure you're choosing the groups you think you are choosing - you not copying relevant parts of your terminal output into emails is making things difficult. Mark Am I wrong? Thanks, SN On Thu, Apr 28, 2011 at 8:29 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 4/29/2011 4:08 AM, shivangi nangia wrote: Hello all, I am trying to order the TIP4P water molecules in my system with respect to the polypeptide in my system. The command I am using is: trjorder -f shape.gro -s shape.tpr -da 0 -na 4 -o ordered.gro This runs without any error and ordered.gro is generated with random sequence of water molecules. Just to cross check I calculated the distances between one of atoms of the polypeptide and oxyegn atom of different ordered water molecules. I found, there is no ascendig trend in the distances with respect to the polypeptide as a go down in the ordered.gro file. What could be going wrong? -da 0 has a particular effect - is it appropriate? Did you choose the right groups? You could use the -nshell option to probe what trjorder thinks is going on. Mark -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read
[gmx-users] trjorder not working
Hello all, I am trying to order the TIP4P water molecules in my system with respect to the polypeptide in my system. The command I am using is: trjorder -f shape.gro -s shape.tpr -da 0 -na 4 -o ordered.gro This runs without any error and ordered.gro is generated with random sequence of water molecules. Just to cross check I calculated the distances between one of atoms of the polypeptide and oxyegn atom of different ordered water molecules. I found, there is no ascendig trend in the distances with respect to the polypeptide as a go down in the ordered.gro file. What could be going wrong? Thanks, SN -- 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] trjorder not working
On 4/29/2011 4:08 AM, shivangi nangia wrote: Hello all, I am trying to order the TIP4P water molecules in my system with respect to the polypeptide in my system. The command I am using is: trjorder -f shape.gro -s shape.tpr -da 0 -na 4 -o ordered.gro This runs without any error and ordered.gro is generated with random sequence of water molecules. Just to cross check I calculated the distances between one of atoms of the polypeptide and oxyegn atom of different ordered water molecules. I found, there is no ascendig trend in the distances with respect to the polypeptide as a go down in the ordered.gro file. What could be going wrong? -da 0 has a particular effect - is it appropriate? Did you choose the right groups? You could use the -nshell option to probe what trjorder thinks is going on. Mark -- 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] trjorder not working
Hello, The manual explaining trjorder says: trjorder orders molecules according to the smallest distance to atoms in a reference group or on z-coordinate (with option -z). With distance ordering, it will ask for a group of reference atoms and a group of molecules. For each frame of the trajectory the selected molecules will be reordered according to the shortest distance between atom number -da in the molecule and all the atoms in the reference group. *The center of mass of the molecules can be used instead of a reference atom by setting -da to 0* In order to arrange water molecules in accordance with the COM of the polypeptide, I chose -da 0. Am I wrong? Thanks, SN On Thu, Apr 28, 2011 at 8:29 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/29/2011 4:08 AM, shivangi nangia wrote: Hello all, I am trying to order the TIP4P water molecules in my system with respect to the polypeptide in my system. The command I am using is: trjorder -f shape.gro -s shape.tpr -da 0 -na 4 -o ordered.gro This runs without any error and ordered.gro is generated with random sequence of water molecules. Just to cross check I calculated the distances between one of atoms of the polypeptide and oxyegn atom of different ordered water molecules. I found, there is no ascendig trend in the distances with respect to the polypeptide as a go down in the ordered.gro file. What could be going wrong? -da 0 has a particular effect - is it appropriate? Did you choose the right groups? You could use the -nshell option to probe what trjorder thinks is going on. Mark -- 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] trjorder not working
On 4/29/2011 11:29 AM, shivangi nangia wrote: Hello, The manual explaining trjorder says: trjorder orders molecules according to the smallest distance to atoms in a reference group or on z-coordinate (with option -z). With distance ordering, it will ask for a group of reference atoms and a group of molecules. For each frame of the trajectory the selected molecules will be reordered according to the shortest distance between atom number -da in the molecule and all the atoms in the reference group. *The center of mass of the molecules can be used instead of a reference atom by setting -da to 0* In order to arrange water molecules in accordance with the COM of the polypeptide, I chose -da 0. As it says above, -da refers to an atom or COM of the molecule, not the reference group. This could be worded better in the documentation. Be sure you're choosing the groups you think you are choosing - you not copying relevant parts of your terminal output into emails is making things difficult. Mark Am I wrong? Thanks, SN On Thu, Apr 28, 2011 at 8:29 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 4/29/2011 4:08 AM, shivangi nangia wrote: Hello all, I am trying to order the TIP4P water molecules in my system with respect to the polypeptide in my system. The command I am using is: trjorder -f shape.gro -s shape.tpr -da 0 -na 4 -o ordered.gro This runs without any error and ordered.gro is generated with random sequence of water molecules. Just to cross check I calculated the distances between one of atoms of the polypeptide and oxyegn atom of different ordered water molecules. I found, there is no ascendig trend in the distances with respect to the polypeptide as a go down in the ordered.gro file. What could be going wrong? -da 0 has a particular effect - is it appropriate? Did you choose the right groups? You could use the -nshell option to probe what trjorder thinks is going on. Mark -- 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 the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/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
