Re: [gmx-users] CG Force and Potential through do_force()
- Original Message - From: Sikandar Mashayak symasha...@gmail.com Date: Thursday, March 25, 2010 15:12 Subject: Re: [gmx-users] CG Force and Potential through do_force() To: Discussion list for GROMACS users gmx-users@gromacs.org well if I need to add it by myself, I am not very sure in what variable to add it to. Like I said, I know to add the force on the atom i do f[indxofatom][XX]= forcevalue, where to potential value due to this force? It's not easy. Look at how the generic kernel does it and work you way back through the data structures. Mark On Wed, Mar 24, 2010 at 10:52 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 25/03/2010 2:42 PM, Sikandar Mashayak wrote: Hi I want to do Coarse-Grained simulation in Gromacs. I have one CG force formula, which I plan to implement by adding a short code in do_force() routine in Gromacs 4.0.7 source code. After browsing through the do_force() code, I am now familiar with data structure relevant to add the new force. I mean, I can specify new force by adding to f[indx][XX] and so on. But I am not very sure about potential, whether do I have to explicitly specify the potential on atoms due to this force or gromacs automatically takes care of it by knowing the forces on each atoms? You will need to add that yourself if you want the reported potential to be accurate. GROMACS uses the given parameters in its inner loops to calculate energies and forces. The former are not reverse-engineered from the latter. If the potential is never used, however, then you can forget about it... Mark -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] CG Force and Potential through do_force()
If your force is between atom pairs you might be better trying to give all of that as a tabulated potential ... no coding. On Mar 25, 2010, at 7:14 AM, Mark Abraham wrote: - Original Message - From: Sikandar Mashayak symasha...@gmail.com Date: Thursday, March 25, 2010 15:12 Subject: Re: [gmx-users] CG Force and Potential through do_force() To: Discussion list for GROMACS users gmx-users@gromacs.org well if I need to add it by myself, I am not very sure in what variable to add it to. Like I said, I know to add the force on the atom i do f[indxofatom][XX]= forcevalue, where to potential value due to this force? It's not easy. Look at how the generic kernel does it and work you way back through the data structures. Mark On Wed, Mar 24, 2010 at 10:52 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 25/03/2010 2:42 PM, Sikandar Mashayak wrote: Hi I want to do Coarse-Grained simulation in Gromacs. I have one CG force formula, which I plan to implement by adding a short code in do_force() routine in Gromacs 4.0.7 source code. After browsing through the do_force() code, I am now familiar with data structure relevant to add the new force. I mean, I can specify new force by adding to f[indx][XX] and so on. But I am not very sure about potential, whether do I have to explicitly specify the potential on atoms due to this force or gromacs automatically takes care of it by knowing the forces on each atoms? You will need to add that yourself if you want the reported potential to be accurate. GROMACS uses the given parameters in its inner loops to calculate energies and forces. The former are not reverse-engineered from the latter. If the potential is never used, however, then you can forget about it... 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] CG Force and Potential through do_force()
@ Mark :: you said if the potential is never used then I dont have to worry about storing its value. Suppose I am replacing Coulombic interactions with something of its equivalent through new force field, and I dont store the potential due to it, will I still get the similar results in terms of structure (RDF). Of course I am assuming that new force can accurately replace the Coulombic interactions among the charged atoms. By just having correct forces acting on the atoms and not worrying about storing potential energies, will I still get same trajectory as with storing potential energies. thanks sikandar On Thu, Mar 25, 2010 at 5:45 AM, XAvier Periole x.peri...@rug.nl wrote: If your force is between atom pairs you might be better trying to give all of that as a tabulated potential ... no coding. On Mar 25, 2010, at 7:14 AM, Mark Abraham wrote: - Original Message - From: Sikandar Mashayak symasha...@gmail.com Date: Thursday, March 25, 2010 15:12 Subject: Re: [gmx-users] CG Force and Potential through do_force() To: Discussion list for GROMACS users gmx-users@gromacs.org well if I need to add it by myself, I am not very sure in what variable to add it to. Like I said, I know to add the force on the atom i do f[indxofatom][XX]= forcevalue, where to potential value due to this force? It's not easy. Look at how the generic kernel does it and work you way back through the data structures. Mark On Wed, Mar 24, 2010 at 10:52 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 25/03/2010 2:42 PM, Sikandar Mashayak wrote: Hi I want to do Coarse-Grained simulation in Gromacs. I have one CG force formula, which I plan to implement by adding a short code in do_force() routine in Gromacs 4.0.7 source code. After browsing through the do_force() code, I am now familiar with data structure relevant to add the new force. I mean, I can specify new force by adding to f[indx][XX] and so on. But I am not very sure about potential, whether do I have to explicitly specify the potential on atoms due to this force or gromacs automatically takes care of it by knowing the forces on each atoms? You will need to add that yourself if you want the reported potential to be accurate. GROMACS uses the given parameters in its inner loops to calculate energies and forces. The former are not reverse-engineered from the latter. If the potential is never used, however, then you can forget about it... 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] CG Force and Potential through do_force()
@ Xavier :: I am trying out table approach also. But I am facing some issues with it. To start with , as a test run, i use GROMACS provided table6-12.xvg table for LJ interactions. Using this table I am running water bulk simulations. In mdp file I specify to use PME for electrostatics and User for LJ by providing the table6-12.xvg file. But the simulation crashes with the notes ::t = 0.000 ps: Water molecule starting at atom 5363 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates thanks sikandar On Thu, Mar 25, 2010 at 11:26 AM, Sikandar Mashayak symasha...@gmail.comwrote: @ Mark :: you said if the potential is never used then I dont have to worry about storing its value. Suppose I am replacing Coulombic interactions with something of its equivalent through new force field, and I dont store the potential due to it, will I still get the similar results in terms of structure (RDF). Of course I am assuming that new force can accurately replace the Coulombic interactions among the charged atoms. By just having correct forces acting on the atoms and not worrying about storing potential energies, will I still get same trajectory as with storing potential energies. thanks sikandar On Thu, Mar 25, 2010 at 5:45 AM, XAvier Periole x.peri...@rug.nl wrote: If your force is between atom pairs you might be better trying to give all of that as a tabulated potential ... no coding. On Mar 25, 2010, at 7:14 AM, Mark Abraham wrote: - Original Message - From: Sikandar Mashayak symasha...@gmail.com Date: Thursday, March 25, 2010 15:12 Subject: Re: [gmx-users] CG Force and Potential through do_force() To: Discussion list for GROMACS users gmx-users@gromacs.org well if I need to add it by myself, I am not very sure in what variable to add it to. Like I said, I know to add the force on the atom i do f[indxofatom][XX]= forcevalue, where to potential value due to this force? It's not easy. Look at how the generic kernel does it and work you way back through the data structures. Mark On Wed, Mar 24, 2010 at 10:52 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 25/03/2010 2:42 PM, Sikandar Mashayak wrote: Hi I want to do Coarse-Grained simulation in Gromacs. I have one CG force formula, which I plan to implement by adding a short code in do_force() routine in Gromacs 4.0.7 source code. After browsing through the do_force() code, I am now familiar with data structure relevant to add the new force. I mean, I can specify new force by adding to f[indx][XX] and so on. But I am not very sure about potential, whether do I have to explicitly specify the potential on atoms due to this force or gromacs automatically takes care of it by knowing the forces on each atoms? You will need to add that yourself if you want the reported potential to be accurate. GROMACS uses the given parameters in its inner loops to calculate energies and forces. The former are not reverse-engineered from the latter. If the potential is never used, however, then you can forget about it... 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org
Re: [gmx-users] CG Force and Potential through do_force()
On 26/03/2010 3:26 AM, Sikandar Mashayak wrote: @ Mark :: you said if the potential is never used then I dont have to worry about storing its value. Suppose I am replacing Coulombic interactions with something of its equivalent through new force field, and I dont store the potential due to it, will I still get the similar results in terms of structure (RDF). Of course I am assuming that new force can accurately replace the Coulombic interactions among the charged atoms. By just having correct forces acting on the atoms and not worrying about storing potential energies, will I still get same trajectory as with storing potential energies. Yes, if the potential is never used. In principle, MD is integrating Newton's Laws, which generally don't require the energy to be known. Whether that is true depends on details of your simulation protocol that we don't know. REMD, being a Monte Carlo method, needs an accurate potential. Free-energy methods might need an accurate potential. Generally speaking, equilibrium MD doesn't need it, however. You can roughly test for this by adding some arbitrarily large value to the energy (e.g. 10^90) and see if the subsequent MD breaks. First, do your homework about how the algorithms you're using work... :-) Mark On Thu, Mar 25, 2010 at 5:45 AM, XAvier Periole x.peri...@rug.nl mailto:x.peri...@rug.nl wrote: If your force is between atom pairs you might be better trying to give all of that as a tabulated potential ... no coding. On Mar 25, 2010, at 7:14 AM, Mark Abraham wrote: - Original Message - From: Sikandar Mashayak symasha...@gmail.com mailto:symasha...@gmail.com Date: Thursday, March 25, 2010 15:12 Subject: Re: [gmx-users] CG Force and Potential through do_force() To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org well if I need to add it by myself, I am not very sure in what variable to add it to. Like I said, I know to add the force on the atom i do f[indxofatom][XX]= forcevalue, where to potential value due to this force? It's not easy. Look at how the generic kernel does it and work you way back through the data structures. Mark On Wed, Mar 24, 2010 at 10:52 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 25/03/2010 2:42 PM, Sikandar Mashayak wrote: Hi I want to do Coarse-Grained simulation in Gromacs. I have one CG force formula, which I plan to implement by adding a short code in do_force() routine in Gromacs 4.0.7 source code. After browsing through the do_force() code, I am now familiar with data structure relevant to add the new force. I mean, I can specify new force by adding to f[indx][XX] and so on. But I am not very sure about potential, whether do I have to explicitly specify the potential on atoms due to this force or gromacs automatically takes care of it by knowing the forces on each atoms? You will need to add that yourself if you want the reported potential to be accurate. GROMACS uses the given parameters in its inner loops to calculate energies and forces. The former are not reverse-engineered from the latter. If the potential is never used, however, then you can forget about it... 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use
Re: [gmx-users] CG Force and Potential through do_force()
On 26/03/2010 7:07 AM, Sikandar Mashayak wrote: @ Xavier :: I am trying out table approach also. But I am facing some issues with it. To start with , as a test run, i use GROMACS provided table6-12.xvg table for LJ interactions. Using this table I am running water bulk simulations. In mdp file I specify to use PME for electrostatics and User for LJ by providing the table6-12.xvg file. But the simulation crashes with the notes ::t = 0.000 ps: Water molecule starting at atom 5363 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Did it run without using tables? Mark On Thu, Mar 25, 2010 at 11:26 AM, Sikandar Mashayak symasha...@gmail.com mailto:symasha...@gmail.com wrote: @ Mark :: you said if the potential is never used then I dont have to worry about storing its value. Suppose I am replacing Coulombic interactions with something of its equivalent through new force field, and I dont store the potential due to it, will I still get the similar results in terms of structure (RDF). Of course I am assuming that new force can accurately replace the Coulombic interactions among the charged atoms. By just having correct forces acting on the atoms and not worrying about storing potential energies, will I still get same trajectory as with storing potential energies. thanks sikandar On Thu, Mar 25, 2010 at 5:45 AM, XAvier Periole x.peri...@rug.nl mailto:x.peri...@rug.nl wrote: If your force is between atom pairs you might be better trying to give all of that as a tabulated potential ... no coding. On Mar 25, 2010, at 7:14 AM, Mark Abraham wrote: - Original Message - From: Sikandar Mashayak symasha...@gmail.com mailto:symasha...@gmail.com Date: Thursday, March 25, 2010 15:12 Subject: Re: [gmx-users] CG Force and Potential through do_force() To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org well if I need to add it by myself, I am not very sure in what variable to add it to. Like I said, I know to add the force on the atom i do f[indxofatom][XX]= forcevalue, where to potential value due to this force? It's not easy. Look at how the generic kernel does it and work you way back through the data structures. Mark On Wed, Mar 24, 2010 at 10:52 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 25/03/2010 2:42 PM, Sikandar Mashayak wrote: Hi I want to do Coarse-Grained simulation in Gromacs. I have one CG force formula, which I plan to implement by adding a short code in do_force() routine in Gromacs 4.0.7 source code. After browsing through the do_force() code, I am now familiar with data structure relevant to add the new force. I mean, I can specify new force by adding to f[indx][XX] and so on. But I am not very sure about potential, whether do I have to explicitly specify the potential on atoms due to this force or gromacs automatically takes care of it by knowing the forces on each atoms? You will need to add that yourself if you want the reported potential to be accurate. GROMACS uses the given parameters in its inner loops to calculate energies and forces. The former are not reverse-engineered from the latter. If the potential is never used, however, then you can forget about it... 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx
[gmx-users] CG Force and Potential through do_force()
Hi I want to do Coarse-Grained simulation in Gromacs. I have one CG force formula, which I plan to implement by adding a short code in do_force() routine in Gromacs 4.0.7 source code. After browsing through the do_force() code, I am now familiar with data structure relevant to add the new force. I mean, I can specify new force by adding to f[indx][XX] and so on. But I am not very sure about potential, whether do I have to explicitly specify the potential on atoms due to this force or gromacs automatically takes care of it by knowing the forces on each atoms? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] CG Force and Potential through do_force()
well if I need to add it by myself, I am not very sure in what variable to add it to. Like I said, I know to add the force on the atom i do f[indxofatom][XX]= forcevalue, where to potential value due to this force? thanks sikandar On Wed, Mar 24, 2010 at 10:52 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 25/03/2010 2:42 PM, Sikandar Mashayak wrote: Hi I want to do Coarse-Grained simulation in Gromacs. I have one CG force formula, which I plan to implement by adding a short code in do_force() routine in Gromacs 4.0.7 source code. After browsing through the do_force() code, I am now familiar with data structure relevant to add the new force. I mean, I can specify new force by adding to f[indx][XX] and so on. But I am not very sure about potential, whether do I have to explicitly specify the potential on atoms due to this force or gromacs automatically takes care of it by knowing the forces on each atoms? You will need to add that yourself if you want the reported potential to be accurate. GROMACS uses the given parameters in its inner loops to calculate energies and forces. The former are not reverse-engineered from the latter. If the potential is never used, however, then you can forget about it... 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
