Re: [gmx-users] Shift electrostatic summation
Shuangxing Dai wrote: Dear all, I was trying to modify the Shift option of electrostatic summation. Mainly I want to modify the formulas of this electrostatic summation. From the manual page 69, the modified non-bonded interactions, the formulas about Shift is there. In the file /src/gmxlib/shift_util.c, there are these formulas. So is this the only file for Shift? Since I have added some printf lines to this file, I do not see the result when I recompile and use Shift. I doubt whether this function was called to do Shift. Or is there any other file related with the Shift method and I need to change? It won't be called... the routines in src/gmxlib/nonbonded/xxx are used. The easiest way to experiment with changes to (nonbonded) interactions is to use table potentials. See various sections of the manual. 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] Shift electrostatic summation
Dear all, I was trying to modify the Shift option of electrostatic summation. Mainly I want to modify the formulas of this electrostatic summation. From the manual page 69, the modified non-bonded interactions, the formulas about Shift is there. In the file /src/gmxlib/shift_util.c, there are these formulas. So is this the only file for Shift? Since I have added some printf lines to this file, I do not see the result when I recompile and use Shift. I doubt whether this function was called to do Shift. Or is there any other file related with the Shift method and I need to change? Thanks in advance. -- Shuangxing Dai ___ 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] Shift Electrostatic Summation
Thank you for your advice and sorry for the misinterpretation. The N is the total number of the system and E^Mad_tot is the total energy for the system. The outer loop sums over all the ions and the inner one sums over the neighbours in the cut-off radius. So it is difficult to decompose this total energy to the summation of pair potential since the self energy part is not easy to decompose. I will follow your advice. Thanks again. Shuangxing Dai - Original Message - From: "Mark Abraham" To: "Discussion list for GROMACS users" Sent: 14 April, 2009 10:21 PM Subject: Re: [gmx-users] Shift Electrostatic Summation Shuangxing Dai wrote: - Original Message - From: "Mark Abraham" To: "Discussion list for GROMACS users" Sent: 14 April, 2009 8:01 PM Subject: Re: [gmx-users] Shift Electrostatic Summation Shuangxing Dai wrote: Thank you for your help. Yes, when I found the user define part for electrostatics, I hope I can use this part since the analytic form of my potential is known. However, since there is a self energy term exist and then the whole energy cannot be decomposed to pair interactions because I cannot specify how much to each pair since the number of neighbours is unkown. That is why I am confused. So I still need an new electrostatic summation similiar to shift, not just a new pair interaction. The number of neighbours is known at run-time. However, I still don't see why this matters - see http://www.gromacs.org/pipermail/gmx-users/2009-March/040830.html OK, the self energy is assigned for each ion. If I want to decompose the potential form of total energy to summation of pair potential, I should devide the self term by number of neighbours and assigned to each pair. So I cannot use user define potential for my problem. You can use a user potential if the dependence of the force and/or potential on r and N is sufficiently separable. The number of neighbours is known inside the inner nonbonded loops, because they're looping over the neighbours of each particle. So you merely do a table lookup before or after some function of N is applied to some function of r. Thus the only work you'd need to do is to construct the correct form of tables, and add in the arithmetic concerning N. Per my advice in that previous thread, you should read and understand the code for the nonbonded kernel for a straight cutoff, compare that with non-table-lookup Ewald, and compare that with table-lookup Ewald. Also heed the advice Berk gave you. You've still never explained why N in the formula in that previous thread is the number of neighbours of a given particle, not the number of particles in the system - but that's your problem. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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] Shift Electrostatic Summation
Shuangxing Dai wrote: Thank you for your help. Yes, when I found the user define part for electrostatics, I hope I can use this part since the analytic form of my potential is known. However, since there is a self energy term exist and then the whole energy cannot be decomposed to pair interactions because I cannot specify how much to each pair since the number of neighbours is unkown. That is why I am confused. So I still need an new electrostatic summation similiar to shift, not just a new pair interaction. And I cannot understand/find how the force for Shift electrostatic summation is calculated in force.c since there is no formula for force found. Or I find the wrong place? And if I want to modify the force formula for Shift, where is it? This is because we use tables internally for this as well. The tables are generated in tables.c. However you may want to look at the self energy correction routines for shift functions (I think it is called shift_util.c). Decomposing energy is a very tricky business, and in most cases does not give you any meaningful results. Thank you for your help. Shuangxing Dai - Original Message - From: "Mark Abraham" To: "Discussion list for GROMACS users" Sent: 14 April, 2009 12:46 AM Subject: Re: [gmx-users] Shift Electrostatic Summation Shuangxing Dai wrote: Hi, all, I was wondering to modify Shift electrostatic summation to a new one. The origin Shift form in Gromacs is like 1/r-1/Rc (Rc is cut-off), I need to modify to erfc(alpha*r)/r-erfc(alpha*Rc)/Rc, and the original long-range correction of Shift in code shift_util.c is q^2/(2*Rc) ( something like that ), I need to q^2*(erfc(alpha*Rc)/(2*Rc)+alpha/sqrt(pi)). So question is: How the force to Shift was calculated? Gromacs use the differentiation to energy, got the force formula, then calculated the force? Or just use the numerical differentiation to the energy and got it? If is the latter one, I do not need to modify the force calculation. GROMACS uses exclusively analytic rather than numerical forces. Probably table lookups as used for PME are the technique you will want to implement. You won't need to change any code if your functions are suitably continuous functions of r and constant parameters. See the tabulated potentials section in the manual. And also, the alpha for Ewald summation, is there an option or parameters to adjust this value? Yes - see the Ewald section of the manual. Also search the mailing list, as this has been discussed several times. Hi, Mark and Berk, if I want do modify shift electrostatic summation as I want, what other files or place do I need to modify, except shift_util.c and force.c? Don't - use table lookups. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Shift Electrostatic Summation
Shuangxing Dai wrote: - Original Message - From: "Mark Abraham" To: "Discussion list for GROMACS users" Sent: 14 April, 2009 8:01 PM Subject: Re: [gmx-users] Shift Electrostatic Summation Shuangxing Dai wrote: Thank you for your help. Yes, when I found the user define part for electrostatics, I hope I can use this part since the analytic form of my potential is known. However, since there is a self energy term exist and then the whole energy cannot be decomposed to pair interactions because I cannot specify how much to each pair since the number of neighbours is unkown. That is why I am confused. So I still need an new electrostatic summation similiar to shift, not just a new pair interaction. The number of neighbours is known at run-time. However, I still don't see why this matters - see http://www.gromacs.org/pipermail/gmx-users/2009-March/040830.html OK, the self energy is assigned for each ion. If I want to decompose the potential form of total energy to summation of pair potential, I should devide the self term by number of neighbours and assigned to each pair. So I cannot use user define potential for my problem. You can use a user potential if the dependence of the force and/or potential on r and N is sufficiently separable. The number of neighbours is known inside the inner nonbonded loops, because they're looping over the neighbours of each particle. So you merely do a table lookup before or after some function of N is applied to some function of r. Thus the only work you'd need to do is to construct the correct form of tables, and add in the arithmetic concerning N. Per my advice in that previous thread, you should read and understand the code for the nonbonded kernel for a straight cutoff, compare that with non-table-lookup Ewald, and compare that with table-lookup Ewald. Also heed the advice Berk gave you. You've still never explained why N in the formula in that previous thread is the number of neighbours of a given particle, not the number of particles in the system - but that's your problem. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Shift Electrostatic Summation
- Original Message - From: "Mark Abraham" To: "Discussion list for GROMACS users" Sent: 14 April, 2009 8:01 PM Subject: Re: [gmx-users] Shift Electrostatic Summation Shuangxing Dai wrote: Thank you for your help. Yes, when I found the user define part for electrostatics, I hope I can use this part since the analytic form of my potential is known. However, since there is a self energy term exist and then the whole energy cannot be decomposed to pair interactions because I cannot specify how much to each pair since the number of neighbours is unkown. That is why I am confused. So I still need an new electrostatic summation similiar to shift, not just a new pair interaction. The number of neighbours is known at run-time. However, I still don't see why this matters - see http://www.gromacs.org/pipermail/gmx-users/2009-March/040830.html OK, the self energy is assigned for each ion. If I want to decompose the potential form of total energy to summation of pair potential, I should devide the self term by number of neighbours and assigned to each pair. So I cannot use user define potential for my problem. And I cannot understand/find how the force for Shift electrostatic summation is calculated in force.c since there is no formula for force found. Or I find the wrong place? And if I want to modify the force formula for Shift, where is it? Look in the nonbonded kernels - like I said in the above post and previously. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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] Shift Electrostatic Summation
Shuangxing Dai wrote: Thank you for your help. Yes, when I found the user define part for electrostatics, I hope I can use this part since the analytic form of my potential is known. However, since there is a self energy term exist and then the whole energy cannot be decomposed to pair interactions because I cannot specify how much to each pair since the number of neighbours is unkown. That is why I am confused. So I still need an new electrostatic summation similiar to shift, not just a new pair interaction. The number of neighbours is known at run-time. However, I still don't see why this matters - see http://www.gromacs.org/pipermail/gmx-users/2009-March/040830.html And I cannot understand/find how the force for Shift electrostatic summation is calculated in force.c since there is no formula for force found. Or I find the wrong place? And if I want to modify the force formula for Shift, where is it? Look in the nonbonded kernels - like I said in the above post and previously. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Shift Electrostatic Summation
Thank you for your help. Yes, when I found the user define part for electrostatics, I hope I can use this part since the analytic form of my potential is known. However, since there is a self energy term exist and then the whole energy cannot be decomposed to pair interactions because I cannot specify how much to each pair since the number of neighbours is unkown. That is why I am confused. So I still need an new electrostatic summation similiar to shift, not just a new pair interaction. And I cannot understand/find how the force for Shift electrostatic summation is calculated in force.c since there is no formula for force found. Or I find the wrong place? And if I want to modify the force formula for Shift, where is it? Thank you for your help. Shuangxing Dai - Original Message - From: "Mark Abraham" To: "Discussion list for GROMACS users" Sent: 14 April, 2009 12:46 AM Subject: Re: [gmx-users] Shift Electrostatic Summation Shuangxing Dai wrote: Hi, all, I was wondering to modify Shift electrostatic summation to a new one. The origin Shift form in Gromacs is like 1/r-1/Rc (Rc is cut-off), I need to modify to erfc(alpha*r)/r-erfc(alpha*Rc)/Rc, and the original long-range correction of Shift in code shift_util.c is q^2/(2*Rc) ( something like that ), I need to q^2*(erfc(alpha*Rc)/(2*Rc)+alpha/sqrt(pi)). So question is: How the force to Shift was calculated? Gromacs use the differentiation to energy, got the force formula, then calculated the force? Or just use the numerical differentiation to the energy and got it? If is the latter one, I do not need to modify the force calculation. GROMACS uses exclusively analytic rather than numerical forces. Probably table lookups as used for PME are the technique you will want to implement. You won't need to change any code if your functions are suitably continuous functions of r and constant parameters. See the tabulated potentials section in the manual. And also, the alpha for Ewald summation, is there an option or parameters to adjust this value? Yes - see the Ewald section of the manual. Also search the mailing list, as this has been discussed several times. Hi, Mark and Berk, if I want do modify shift electrostatic summation as I want, what other files or place do I need to modify, except shift_util.c and force.c? Don't - use table lookups. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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] Shift Electrostatic Summation
Shuangxing Dai wrote: Hi, all, I was wondering to modify Shift electrostatic summation to a new one. The origin Shift form in Gromacs is like 1/r-1/Rc (Rc is cut-off), I need to modify to erfc(alpha*r)/r-erfc(alpha*Rc)/Rc, and the original long-range correction of Shift in code shift_util.c is q^2/(2*Rc) ( something like that ), I need to q^2*(erfc(alpha*Rc)/(2*Rc)+alpha/sqrt(pi)). So question is: How the force to Shift was calculated? Gromacs use the differentiation to energy, got the force formula, then calculated the force? Or just use the numerical differentiation to the energy and got it? If is the latter one, I do not need to modify the force calculation. GROMACS uses exclusively analytic rather than numerical forces. Probably table lookups as used for PME are the technique you will want to implement. You won't need to change any code if your functions are suitably continuous functions of r and constant parameters. See the tabulated potentials section in the manual. And also, the alpha for Ewald summation, is there an option or parameters to adjust this value? Yes - see the Ewald section of the manual. Also search the mailing list, as this has been discussed several times. Hi, Mark and Berk, if I want do modify shift electrostatic summation as I want, what other files or place do I need to modify, except shift_util.c and force.c? Don't - use table lookups. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Shift Electrostatic Summation
Shuangxing Dai wrote: Hi, all, I was wondering to modify Shift electrostatic summation to a new one. The origin Shift form in Gromacs is like 1/r-1/Rc (Rc is cut-off), I need to modify to erfc(alpha*r)/r-erfc(alpha*Rc)/Rc, and the original long-range correction of Shift in code shift_util.c is q^2/(2*Rc) ( something like that ), I need to q^2*(erfc(alpha*Rc)/(2*Rc)+alpha/sqrt(pi)). So question is: How the force to Shift was calculated? Gromacs use the differentiation to energy, got the force formula, then calculated the force? Or just use the numerical differentiation to the energy and got it? If is the latter one, I do not need to modify the force calculation. And also, the alpha for Ewald summation, is there an option or parameters to adjust this value? Hi, Mark and Berk, if I want do modify shift electrostatic summation as I want, what other files or place do I need to modify, except shift_util.c and force.c? Shuangxing Dai It would be wise to test everything with a table look up. Much easier, and the better performance than analytical potentials. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Shift Electrostatic Summation
Hi, all, I was wondering to modify Shift electrostatic summation to a new one. The origin Shift form in Gromacs is like 1/r-1/Rc (Rc is cut-off), I need to modify to erfc(alpha*r)/r-erfc(alpha*Rc)/Rc, and the original long-range correction of Shift in code shift_util.c is q^2/(2*Rc) ( something like that ), I need to q^2*(erfc(alpha*Rc)/(2*Rc)+alpha/sqrt(pi)). So question is: How the force to Shift was calculated? Gromacs use the differentiation to energy, got the force formula, then calculated the force? Or just use the numerical differentiation to the energy and got it? If is the latter one, I do not need to modify the force calculation. And also, the alpha for Ewald summation, is there an option or parameters to adjust this value? Hi, Mark and Berk, if I want do modify shift electrostatic summation as I want, what other files or place do I need to modify, except shift_util.c and force.c? Shuangxing Dai___ gmx-users mailing listgmx-users@gromacs.org http://www.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
