[gmx-users] decomposing the energy
Hello gmx users: I did 1ns simulation for my system and have the trajectory and energy files. Now i want to see the energy of some specific residues. So, i decompose(separated) the energy groups and edited the mdp file. Using the mdp file, i created a new tpr file and rerun the mdrun using the trajectory file. But when i compared the total energy between the old and new one, it differs a lot. I am doing some mistakes somewhere. Can anyone help me please. Thanks. Rama -- 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] decomposing the energy
Ramachandran G wrote: Hello gmx users: I did 1ns simulation for my system and have the trajectory and energy files. Now i want to see the energy of some specific residues. So, i decompose(separated) the energy groups and edited the mdp file. Using the mdp file, i created a new tpr file and rerun the mdrun using the trajectory file. But when i compared the total energy between the old and new one, it differs a lot. I am doing some mistakes somewhere. Can anyone help me please. Thanks. Maybe, maybe not. Without seeing the .mdp settings and the data that you're looking at, all anyone can do is guess. You also haven't stated what type of trajectory (i.e. .xtc or .trr) you're using as -rerun input. If you're using an .xtc file, there is no velocity information, so any property related to velocities (most notably kinetic energy, but several others as well) will be zero. I suspect this is probably where the discrepancy is, but it is not a problem. Using energygrps is only useful for decomposing short-range nonbonded energy terms, nothing else. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] decomposing the energy
On 14/05/2011 9:11 PM, Justin A. Lemkul wrote: Ramachandran G wrote: Hello gmx users: I did 1ns simulation for my system and have the trajectory and energy files. Now i want to see the energy of some specific residues. So, i decompose(separated) the energy groups and edited the mdp file. Using the mdp file, i created a new tpr file and rerun the mdrun using the trajectory file. But when i compared the total energy between the old and new one, it differs a lot. I am doing some mistakes somewhere. Can anyone help me please. Thanks. Maybe, maybe not. Without seeing the .mdp settings and the data that you're looking at, all anyone can do is guess. You also haven't stated what type of trajectory (i.e. .xtc or .trr) you're using as -rerun input. If you're using an .xtc file, there is no velocity information, so any property related to velocities (most notably kinetic energy, but several others as well) will be zero. I suspect this is probably where the discrepancy is, but it is not a problem. Using energygrps is only useful for decomposing short-range nonbonded energy terms, nothing else. Strictly speaking, one can decompose bonded energy terms too, with a well-constructed topology, but I agree with the rest of what Justin said. 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] decomposing the energy
Two things you have to be careful about: 1- use trr trajectory files. xtc precision is not sufficient and it will give a lot of discrepancies at least for the bonded terms. 2- set the nstlist to 1 as the neiboring list should be undated for each frame and not every 5/10 as it is normally set in a regular mdp file. On May 14, 2011, at 1:11 PM, Justin A. Lemkul wrote: Ramachandran G wrote: Hello gmx users: I did 1ns simulation for my system and have the trajectory and energy files. Now i want to see the energy of some specific residues. So, i decompose(separated) the energy groups and edited the mdp file. Using the mdp file, i created a new tpr file and rerun the mdrun using the trajectory file. But when i compared the total energy between the old and new one, it differs a lot. I am doing some mistakes somewhere. Can anyone help me please. Thanks. Maybe, maybe not. Without seeing the .mdp settings and the data that you're looking at, all anyone can do is guess. You also haven't stated what type of trajectory (i.e. .xtc or .trr) you're using as -rerun input. If you're using an .xtc file, there is no velocity information, so any property related to velocities (most notably kinetic energy, but several others as well) will be zero. I suspect this is probably where the discrepancy is, but it is not a problem. Using energygrps is only useful for decomposing short- range nonbonded energy terms, nothing else. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] decomposing the energy
On 14/05/2011 10:52 PM, XAvier Periole wrote: Two things you have to be careful about: 1- use trr trajectory files. xtc precision is not sufficient and it will give a lot of discrepancies at least for the bonded terms. 2- set the nstlist to 1 as the neiboring list should be undated for each frame and not every 5/10 as it is normally set in a regular mdp file. Reruns do neighbour searching every frame, regardless. Mark On May 14, 2011, at 1:11 PM, Justin A. Lemkul wrote: Ramachandran G wrote: Hello gmx users: I did 1ns simulation for my system and have the trajectory and energy files. Now i want to see the energy of some specific residues. So, i decompose(separated) the energy groups and edited the mdp file. Using the mdp file, i created a new tpr file and rerun the mdrun using the trajectory file. But when i compared the total energy between the old and new one, it differs a lot. I am doing some mistakes somewhere. Can anyone help me please. Thanks. Maybe, maybe not. Without seeing the .mdp settings and the data that you're looking at, all anyone can do is guess. You also haven't stated what type of trajectory (i.e. .xtc or .trr) you're using as -rerun input. If you're using an .xtc file, there is no velocity information, so any property related to velocities (most notably kinetic energy, but several others as well) will be zero. I suspect this is probably where the discrepancy is, but it is not a problem. Using energygrps is only useful for decomposing short-range nonbonded energy terms, nothing else. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] decomposing the energy
Hey Mark Do you mean removing all bond definitions from topology file, when you say well constructed topology to exclude all bonded-interactions in rerun? thanks sikandar On Sat, May 14, 2011 at 8:01 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 14/05/2011 10:52 PM, XAvier Periole wrote: Two things you have to be careful about: 1- use trr trajectory files. xtc precision is not sufficient and it will give a lot of discrepancies at least for the bonded terms. 2- set the nstlist to 1 as the neiboring list should be undated for each frame and not every 5/10 as it is normally set in a regular mdp file. Reruns do neighbour searching every frame, regardless. Mark On May 14, 2011, at 1:11 PM, Justin A. Lemkul wrote: Ramachandran G wrote: Hello gmx users: I did 1ns simulation for my system and have the trajectory and energy files. Now i want to see the energy of some specific residues. So, i decompose(separated) the energy groups and edited the mdp file. Using the mdp file, i created a new tpr file and rerun the mdrun using the trajectory file. But when i compared the total energy between the old and new one, it differs a lot. I am doing some mistakes somewhere. Can anyone help me please. Thanks. Maybe, maybe not. Without seeing the .mdp settings and the data that you're looking at, all anyone can do is guess. You also haven't stated what type of trajectory (i.e. .xtc or .trr) you're using as -rerun input. If you're using an .xtc file, there is no velocity information, so any property related to velocities (most notably kinetic energy, but several others as well) will be zero. I suspect this is probably where the discrepancy is, but it is not a problem. Using energygrps is only useful for decomposing short-range nonbonded energy terms, nothing else. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] decomposing the energy
On 15/05/2011 12:01 AM, Sikandar Mashayak wrote: Hey Mark Do you mean removing all bond definitions from topology file, when you say well constructed topology to exclude all bonded-interactions in rerun? I said you can decompose the bonded interactions. You can have none by removing all bonded interactions, but that won't save you any significant time, nor serve any other purpose. Mark thanks sikandar On Sat, May 14, 2011 at 8:01 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 14/05/2011 10:52 PM, XAvier Periole wrote: Two things you have to be careful about: 1- use trr trajectory files. xtc precision is not sufficient and it will give a lot of discrepancies at least for the bonded terms. 2- set the nstlist to 1 as the neiboring list should be undated for each frame and not every 5/10 as it is normally set in a regular mdp file. Reruns do neighbour searching every frame, regardless. Mark On May 14, 2011, at 1:11 PM, Justin A. Lemkul wrote: Ramachandran G wrote: Hello gmx users: I did 1ns simulation for my system and have the trajectory and energy files. Now i want to see the energy of some specific residues. So, i decompose(separated) the energy groups and edited the mdp file. Using the mdp file, i created a new tpr file and rerun the mdrun using the trajectory file. But when i compared the total energy between the old and new one, it differs a lot. I am doing some mistakes somewhere. Can anyone help me please. Thanks. Maybe, maybe not. Without seeing the .mdp settings and the data that you're looking at, all anyone can do is guess. You also haven't stated what type of trajectory (i.e. .xtc or .trr) you're using as -rerun input. If you're using an .xtc file, there is no velocity information, so any property related to velocities (most notably kinetic energy, but several others as well) will be zero. I suspect this is probably where the discrepancy is, but it is not a problem. Using energygrps is only useful for decomposing short-range nonbonded energy terms, nothing else. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 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
