[gmx-users] Conversion of charmm36 parameters from namd to gromacs
Hello, I compared the LJ parameters for the interaction Potassium - backbone carbonyl oxygen for CHARMM36 between the Gromacs and NAMD version of the forcefield. I found different numbers for the sigma value i cannot explain to myself: The stock charmm36 implementation has the following LJ parameters for potassium and oxygen: ; atomEmin (kcal/mol)Rmin/2 (A) POT0.0871.76375 O0.1201.7 Converting the above values to units used in gromacs (kJ/mol and nm) and applying standard combination rules this should give the following nonbonded energy parameters: [ pairtypes] ; sig = (Rmin,i/2 + Rmin,j/2)/10 ; eps = sqrt(Emin,i * Emin,j) * 5.184 kcal/kJ ; ijfuncsig (nm)eps (kj/mol) OPOT10.346 0.4275 However, the actual entry for the interaction in GROMACS/charmm36 has the energy minimum at a much smaller distance (epsilon is on the point though!) ; ij func sig (nm)eps (kJ/mol) OPOT10.2820.4275 Can somebody tell me the reason for this huge difference? Is there an error in my calculation? I am trying to convert an NBFIX applied to this specific interaction to gromacs. However, I am not sure how to proceed without doing the reparametrization in gromacs again, because the stock values differ that much. Best regards, Daniel -- Daniel Bauer, M.Sc. TU Darmstadt Computational Biology & Simulation Schnittspahnstr. 2 64287 Darmstadt ba...@cbs.tu-darmstadt.de Don't trust atoms, they make up everything. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Conversion of charmm36 parameters from namd to gromacs
On 12/3/17 4:18 PM, Daniel Bauer wrote: Hello, I compared the LJ parameters for the interaction Potassium - backbone carbonyl oxygen for CHARMM36 between the Gromacs and NAMD version of the forcefield. I found different numbers for the sigma value i cannot explain to myself: The stock charmm36 implementation has the following LJ parameters for potassium and oxygen: ; atomEmin (kcal/mol)Rmin/2 (A) POT0.0871.76375 O0.1201.7 Converting the above values to units used in gromacs (kJ/mol and nm) and applying standard combination rules this should give the following nonbonded energy parameters: [ pairtypes] ; sig = (Rmin,i/2 + Rmin,j/2)/10 ; eps = sqrt(Emin,i * Emin,j) * 5.184 kcal/kJ ; ijfuncsig (nm)eps (kj/mol) OPOT10.346 0.4275 However, the actual entry for the interaction in GROMACS/charmm36 has the energy minimum at a much smaller distance (epsilon is on the point though!) ; ij func sig (nm)eps (kJ/mol) OPOT10.2820.4275 Can somebody tell me the reason for this huge difference? Is there an error in my calculation? I am trying to convert an NBFIX applied to this specific interaction to gromacs. However, I am not sure how to proceed without doing the reparametrization in gromacs again, because the stock values differ that much. This is actually a value that isn't used. [pairtypes] are for 1-4 interactions, which can never occur between a K+ ion and a carbonyl O. The inclusion in the list is just because it's really hard to tell our conversion program to exclude some massive list of impossible interactions. So they get generated. But to your point, you're missing a critical point of the CHARMM parameter format. The full NONBonded parameter entry in par_all36m_prot.prm for carbonyl O is: O 0.00 -0.12 1.70 0.00 -0.12 1.40 The last fields are epsilon and Rmin/2 when that atom type is used in a 1-4 interaction. So -0.12/1.7 is for the normal nonbonded interaction, -0.12/1.4 is for any 1-4 involving O. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Conversion of charmm36 parameters from namd to gromacs
Hello Justin, Thanks for your response. I was under the assumption that entries in [ pairtypes ] are the ones that override standard LJ interactions derived by pairgen. I now know this is a different section. From what you are saying I come to the conclusion that the POT O interaction in charmm36 for gromacs have no custom potential but are derived via combination rules (as they are in namd). Nevertheless, the numbers still dont seem to match: Since we can ignore 1-4 Interactions in charmm36 as well as gromacs for POT-O, the resulting parameters from the namd version are: sig = 0.3463750 nm; eps=0.42750571533 kJ/mol However, combining the entries for O and POT in the atomtypes section of the gromacs version i get something different: [ atomtypes ] O 815.9990000.000 A 0.302905564168 0.50208 POT1939.0983000.000 A 0.314264522824 0.36401 === sig = 0.308585043 nm; eps=0.42750689 kJ/mol Again, the epsilon value is matching the namd version while sigma is still off by about 0.4 A. If my conversion of the namd parameters and combination rules are correct, this would be a problem. The different position of the energy minimum results in a potential energy difference of around 7 kJ/mol for a distance of 0.29 nm (typical distance for POT-O in the selectivity filter of potassium channels, see attached image). Can you give me a source where I can read up on why the values for sigma and epsilon in gromacs are the way they are? It must be more than a direct conversion of the numbers from kcal to kJ. Or did I again made a mistake or took the wrong numbers? Best regards, Daniel On 12/03/2017 11:23 PM, Justin Lemkul wrote: > > > On 12/3/17 4:18 PM, Daniel Bauer wrote: >> Hello, >> >> >> I compared the LJ parameters for the interaction Potassium - backbone >> carbonyl oxygen for CHARMM36 between the Gromacs and NAMD version of the >> forcefield. I found different numbers for the sigma value i cannot >> explain to myself: >> >> >> The stock charmm36 implementation has the following LJ parameters for >> potassium and oxygen: >> >> ; atomEmin (kcal/mol)Rmin/2 (A) >> >> POT0.0871.76375 >> >> O0.1201.7 >> >> >> Converting the above values to units used in gromacs (kJ/mol and nm) and >> applying standard combination rules this should give the following >> nonbonded energy parameters: >> >> [ pairtypes] >> >> ; sig = (Rmin,i/2 + Rmin,j/2)/10 >> >> ; eps = sqrt(Emin,i * Emin,j) * 5.184 kcal/kJ >> >> ; ijfuncsig (nm)eps (kj/mol) >> >> OPOT10.346 0.4275 >> >> However, the actual entry for the interaction in GROMACS/charmm36 has >> the energy minimum at a much smaller distance (epsilon is on the point >> though!) >> >> ; ij func sig (nm)eps (kJ/mol) >> >> OPOT10.2820.4275 >> >> >> Can somebody tell me the reason for this huge difference? Is there an >> error in my calculation? I am trying to convert an NBFIX applied to this >> specific interaction to gromacs. However, I am not sure how to proceed >> without doing the reparametrization in gromacs again, because the stock >> values differ that much. > > This is actually a value that isn't used. [pairtypes] are for 1-4 > interactions, which can never occur between a K+ ion and a carbonyl O. > The inclusion in the list is just because it's really hard to tell our > conversion program to exclude some massive list of impossible > interactions. So they get generated. > > But to your point, you're missing a critical point of the CHARMM > parameter format. The full NONBonded parameter entry in > par_all36m_prot.prm for carbonyl O is: > > O 0.00 -0.12 1.70 0.00 -0.12 1.40 > > The last fields are epsilon and Rmin/2 when that atom type is used in > a 1-4 interaction. So -0.12/1.7 is for the normal nonbonded > interaction, -0.12/1.4 is for any 1-4 involving O. > > -Justin > -- Daniel Bauer, M.Sc. TU Darmstadt Computational Biology & Simulation Schnittspahnstr. 2 64287 Darmstadt ba...@cbs.tu-darmstadt.de Don't trust atoms, they make up everything. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Conversion of charmm36 parameters from namd to gromacs
On 12/4/17 7:47 AM, Daniel Bauer wrote: Hello Justin, Thanks for your response. I was under the assumption that entries in [ pairtypes ] are the ones that override standard LJ interactions derived by pairgen. I now know this is a different section. From what you are saying I come to the conclusion that the POT O interaction in charmm36 for gromacs have no custom potential but are derived via combination rules (as they are in namd). Nevertheless, the numbers still dont seem to match: Since we can ignore 1-4 Interactions in charmm36 as well as gromacs for POT-O, the resulting parameters from the namd version are: sig = 0.3463750 nm; eps=0.42750571533 kJ/mol Can you please share the source of these parameters? There should be no "NAMD version" of anything. The force field files that you should be using are just the CHARMM distribution. The GROMACS port of CHARMM36 comes directly from those files. There is no official NBFIX for POT-O (yet, we do have one but it's not in the official distribution) so the combination rules should prevail. -Justin However, combining the entries for O and POT in the atomtypes section of the gromacs version i get something different: [ atomtypes ] O 815.9990000.000 A 0.302905564168 0.50208 POT1939.0983000.000 A 0.314264522824 0.36401 === sig = 0.308585043 nm; eps=0.42750689 kJ/mol Again, the epsilon value is matching the namd version while sigma is still off by about 0.4 A. If my conversion of the namd parameters and combination rules are correct, this would be a problem. The different position of the energy minimum results in a potential energy difference of around 7 kJ/mol for a distance of 0.29 nm (typical distance for POT-O in the selectivity filter of potassium channels, see attached image). Can you give me a source where I can read up on why the values for sigma and epsilon in gromacs are the way they are? It must be more than a direct conversion of the numbers from kcal to kJ. Or did I again made a mistake or took the wrong numbers? Best regards, Daniel On 12/03/2017 11:23 PM, Justin Lemkul wrote: On 12/3/17 4:18 PM, Daniel Bauer wrote: Hello, I compared the LJ parameters for the interaction Potassium - backbone carbonyl oxygen for CHARMM36 between the Gromacs and NAMD version of the forcefield. I found different numbers for the sigma value i cannot explain to myself: The stock charmm36 implementation has the following LJ parameters for potassium and oxygen: ; atomEmin (kcal/mol)Rmin/2 (A) POT0.0871.76375 O0.1201.7 Converting the above values to units used in gromacs (kJ/mol and nm) and applying standard combination rules this should give the following nonbonded energy parameters: [ pairtypes] ; sig = (Rmin,i/2 + Rmin,j/2)/10 ; eps = sqrt(Emin,i * Emin,j) * 5.184 kcal/kJ ; ijfuncsig (nm)eps (kj/mol) OPOT10.346 0.4275 However, the actual entry for the interaction in GROMACS/charmm36 has the energy minimum at a much smaller distance (epsilon is on the point though!) ; ij func sig (nm)eps (kJ/mol) OPOT10.2820.4275 Can somebody tell me the reason for this huge difference? Is there an error in my calculation? I am trying to convert an NBFIX applied to this specific interaction to gromacs. However, I am not sure how to proceed without doing the reparametrization in gromacs again, because the stock values differ that much. This is actually a value that isn't used. [pairtypes] are for 1-4 interactions, which can never occur between a K+ ion and a carbonyl O. The inclusion in the list is just because it's really hard to tell our conversion program to exclude some massive list of impossible interactions. So they get generated. But to your point, you're missing a critical point of the CHARMM parameter format. The full NONBonded parameter entry in par_all36m_prot.prm for carbonyl O is: O 0.00 -0.12 1.70 0.00 -0.12 1.40 The last fields are epsilon and Rmin/2 when that atom type is used in a 1-4 interaction. So -0.12/1.7 is for the normal nonbonded interaction, -0.12/1.4 is for any 1-4 involving O. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Conversion of charmm36 parameters from namd to gromacs
Hello, I finally found my error in the conversion. As always, the devil is in the detail. I was under the assumption that parameters listed in the original forcefield files (toppar) are also sigma and epsilon values. However, as you know, the original files list Rmin values (and not sigma). With the correct conversion term: eps = Rmin/(10*2^(1/6)) I can now reproduce the conversion of the numbers from the charmm implementation to gromacs (and thus know how to apply my NBFIX for this value). Thanks for your patience and best regards, Daniel On 12/03/2017 10:18 PM, Daniel Bauer wrote: > Hello, > > > I compared the LJ parameters for the interaction Potassium - backbone > carbonyl oxygen for CHARMM36 between the Gromacs and NAMD version of the > forcefield. I found different numbers for the sigma value i cannot > explain to myself: > > > The stock charmm36 implementation has the following LJ parameters for > potassium and oxygen: > > ; atomEmin (kcal/mol)Rmin/2 (A) > > POT0.0871.76375 > > O0.1201.7 > > > Converting the above values to units used in gromacs (kJ/mol and nm) and > applying standard combination rules this should give the following > nonbonded energy parameters: > > [ pairtypes] > > ; sig = (Rmin,i/2 + Rmin,j/2)/10 > > ; eps = sqrt(Emin,i * Emin,j) * 5.184 kcal/kJ > > ; ijfuncsig (nm)eps (kj/mol) > > OPOT10.346 0.4275 > > However, the actual entry for the interaction in GROMACS/charmm36 has > the energy minimum at a much smaller distance (epsilon is on the point > though!) > > ; ij func sig (nm)eps (kJ/mol) > > OPOT10.2820.4275 > > > Can somebody tell me the reason for this huge difference? Is there an > error in my calculation? I am trying to convert an NBFIX applied to this > specific interaction to gromacs. However, I am not sure how to proceed > without doing the reparametrization in gromacs again, because the stock > values differ that much. > > Best regards, > > Daniel > > -- Daniel Bauer, M.Sc. TU Darmstadt Computational Biology & Simulation Schnittspahnstr. 2 64287 Darmstadt ba...@cbs.tu-darmstadt.de Don't trust atoms, they make up everything. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Conversion of charmm36 parameters from namd to gromacs
On 12/4/17 12:21 PM, Daniel Bauer wrote: Hello, I finally found my error in the conversion. As always, the devil is in the detail. I was under the assumption that parameters listed in the original forcefield files (toppar) are also sigma and epsilon values. However, as you know, the original files list Rmin values (and not sigma). With the correct conversion term: eps = Rmin/(10*2^(1/6)) I can now reproduce the conversion of the numbers from the charmm implementation to gromacs (and thus know how to apply my NBFIX for this value). I don't know what NBFIX you might have, but FYI there is a value that will become official in the next release of the force field. We've validated it against proteins and nucleic acids. See the SI of http://dx.doi.org/10.1128/AAC.01572-17 -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Conversion of charmm36 parameters from namd to gromacs
Unfortunatly It seems like my university has no contract to access this paper so I cant check the SI. The ones I have are from http://dx.doi.org/10.7554/eLife.25844 (adjusted to better match the free energy of solvation in NMA). On 12/04/2017 07:53 PM, Justin Lemkul wrote: > > > On 12/4/17 12:21 PM, Daniel Bauer wrote: >> Hello, >> >> I finally found my error in the conversion. As always, the devil is in >> the detail. I was under the assumption that parameters listed in the >> original forcefield files (toppar) are also sigma and epsilon values. >> However, as you know, the original files list Rmin values (and not >> sigma). >> >> With the correct conversion term: >> >> eps = Rmin/(10*2^(1/6)) >> >> I can now reproduce the conversion of the numbers from the charmm >> implementation to gromacs (and thus know how to apply my NBFIX for this >> value). > > I don't know what NBFIX you might have, but FYI there is a value that > will become official in the next release of the force field. We've > validated it against proteins and nucleic acids. See the SI of > http://dx.doi.org/10.1128/AAC.01572-17 > > -Justin > -- Daniel Bauer, M.Sc. TU Darmstadt Computational Biology & Simulation Schnittspahnstr. 2 64287 Darmstadt ba...@cbs.tu-darmstadt.de Don't trust atoms, they make up everything. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Conversion of charmm36 parameters from namd to gromacs
On 12/4/17 2:35 PM, Daniel Bauer wrote: Unfortunatly It seems like my university has no contract to access this paper so I cant check the SI. The ones I have are from http://dx.doi.org/10.7554/eLife.25844 (adjusted to better match the free energy of solvation in NMA). There seem to be several layers of assumption here, including targeting a value that is actually unknown. If you want to compare, in the paper I linked before, we did a QM potential energy scan for NMA...K+ as a function of the distance between the carbonyl O and the ion. The standard CHARMM force field parameters are too weak by about 6 kcal/mol relative to an MP2/6-311++G(2df,2pd) energy surface. The NBFIX we applied to correct it was: epsilon = -0.050218 kcal/mol Rmin = 3.30375 A -Justin On 12/04/2017 07:53 PM, Justin Lemkul wrote: On 12/4/17 12:21 PM, Daniel Bauer wrote: Hello, I finally found my error in the conversion. As always, the devil is in the detail. I was under the assumption that parameters listed in the original forcefield files (toppar) are also sigma and epsilon values. However, as you know, the original files list Rmin values (and not sigma). With the correct conversion term: eps = Rmin/(10*2^(1/6)) I can now reproduce the conversion of the numbers from the charmm implementation to gromacs (and thus know how to apply my NBFIX for this value). I don't know what NBFIX you might have, but FYI there is a value that will become official in the next release of the force field. We've validated it against proteins and nucleic acids. See the SI of http://dx.doi.org/10.1128/AAC.01572-17 -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
