Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa
Darrell Koskinen wrote: Hi Mark, I thought opls_127 and opls_128 were the representative atoms to use for ammonia. Please correct me if I am wrong. I don't know anything more than what's in ffoplsa* files or the papers. Would the adsorption of the polar ammonia molecule onto the polar (hydrogen-terminated) edges of the graphene sheet be affected by the missing LJ parameter on the H atoms? Define "missing". If it is zero by design, that's because zero served the purpose during the parameterization, and the documentation as quoted by you is perhaps erroneous with respect to small molecules. If it oplsa_128 should have non-zero LJ then you'll need to find more evidence of that in the OPLSAA papers, or by consulting the authors. Note that most models of water do not have LJ on the H atoms, and so not having LJ on H atoms of solvated ammonia is probably quite consistent. Doesn't this bring us back to the point of quite a while ago, that an ammonia model that was probably not parameterized for the gas phase might not be useful in the gas phase? Mark Date: Mon, 26 Oct 2009 08:47:14 +1100 From: Mark Abraham Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa To: Discussion list for GROMACS users Message-ID: <4ae4c762.2060...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Justin A. Lemkul wrote: Darrell Koskinen wrote: I looked through the ffoplsaanb.itp file and see that all the H atoms except for the following four have zero LJ parameters: HC OPLS_140 alkane H HA OPLS_146 Benzene H H4 OPLS_345 Cytosine H-C6 H5 OPLS_355 Adenine & Guanine H-C2 However, in the paper "Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids", it states: "The original OPLS (optimized potentials for liquid simulations) potential functions used a partially united-atom (UA) model; sites for nonbonded interactions are placed on all nonhydrogen atoms and on hydrogens attached to heteroatoms or carbons in aromatic rings". Later, the paper indicates that the paramters were adopted as much as possible from the OPLS-UA force field. Thus, since "sites for nonbonded interactions are placed on hydrogens attached to heteroatoms ", it appears to me that a site for a non-bonded interaction should exist on the H atoms within ammonia. Is my interpretation incorrect? I don't think so. Each of the above examples you've cited above is for a C-H bond in an aromatic ring. In OPLS, all N-H bonds involved hydrogen atoms with zero LJ parameters. See, for example, any backbone NH, amide (ASN/GLN), or amine (LYS/LYSH), etc and you will see the atom types used. I think you're both partly wrong. Type 140 is not for C-H in an aromatic ring, and if you grep 1.008 ffoplsaanb.itp you get many more H atom types with LJ. Certainly Justin's right inasmuch as amide N-H type 241 has no H LJ parameters. Perhaps there's other text that Darrell hasn't found yet, or backbone nitrogen is not considered a heteroatom :-). Mark Darrell Date: Mon, 19 Oct 2009 19:07:22 +1100 From: Mark Abraham Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa To: Discussion list for GROMACS users Message-ID: <4adc1e3a.8010...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Hi, I see that the Lennard Jones parameters for the N & H atoms in ammonia, represented by opls_127 and opls_128 in the file ffoplsaanb.itp are: opls_127 NT 7 14.00670-1.020 A3.42000e-01 7.11280e-01 opls_128 H 1 1.00800 0.340 A0.0e+00 0.0e+00 Why are sigma and epsilon both zero for H? Are the LJ parameters for H embedded in the parameter for NT? If so, how were these parameters combined? What do other H have? What do the OPLS-AA paper(s) have to say about such H atoms? 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
Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa
Justin A. Lemkul wrote: Darrell Koskinen wrote: I looked through the ffoplsaanb.itp file and see that all the H atoms except for the following four have zero LJ parameters: HC OPLS_140 alkane H HA OPLS_146 Benzene H H4 OPLS_345 Cytosine H-C6 H5 OPLS_355 Adenine & Guanine H-C2 However, in the paper "Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids", it states: "The original OPLS (optimized potentials for liquid simulations) potential functions used a partially united-atom (UA) model; sites for nonbonded interactions are placed on all nonhydrogen atoms and on hydrogens attached to heteroatoms or carbons in aromatic rings". Later, the paper indicates that the paramters were adopted as much as possible from the OPLS-UA force field. Thus, since "sites for nonbonded interactions are placed on hydrogens attached to heteroatoms ", it appears to me that a site for a non-bonded interaction should exist on the H atoms within ammonia. Is my interpretation incorrect? I don't think so. Each of the above examples you've cited above is for a C-H bond in an aromatic ring. In OPLS, all N-H bonds involved hydrogen atoms with zero LJ parameters. See, for example, any backbone NH, amide (ASN/GLN), or amine (LYS/LYSH), etc and you will see the atom types used. I think you're both partly wrong. Type 140 is not for C-H in an aromatic ring, and if you grep 1.008 ffoplsaanb.itp you get many more H atom types with LJ. Certainly Justin's right inasmuch as amide N-H type 241 has no H LJ parameters. Perhaps there's other text that Darrell hasn't found yet, or backbone nitrogen is not considered a heteroatom :-). Mark Darrell Date: Mon, 19 Oct 2009 19:07:22 +1100 From: Mark Abraham Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa To: Discussion list for GROMACS users Message-ID: <4adc1e3a.8010...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Hi, I see that the Lennard Jones parameters for the N & H atoms in ammonia, represented by opls_127 and opls_128 in the file ffoplsaanb.itp are: opls_127 NT 7 14.00670-1.020 A3.42000e-01 7.11280e-01 opls_128 H 1 1.00800 0.340 A0.0e+00 0.0e+00 Why are sigma and epsilon both zero for H? Are the LJ parameters for H embedded in the parameter for NT? If so, how were these parameters combined? What do other H have? What do the OPLS-AA paper(s) have to say about such H atoms? 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
Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa
Darrell Koskinen wrote: I looked through the ffoplsaanb.itp file and see that all the H atoms except for the following four have zero LJ parameters: HC OPLS_140 alkane H HA OPLS_146 Benzene H H4 OPLS_345 Cytosine H-C6 H5 OPLS_355 Adenine & Guanine H-C2 However, in the paper "Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids", it states: "The original OPLS (optimized potentials for liquid simulations) potential functions used a partially united-atom (UA) model; sites for nonbonded interactions are placed on all nonhydrogen atoms and on hydrogens attached to heteroatoms or carbons in aromatic rings". Later, the paper indicates that the paramters were adopted as much as possible from the OPLS-UA force field. Thus, since "sites for nonbonded interactions are placed on hydrogens attached to heteroatoms ", it appears to me that a site for a non-bonded interaction should exist on the H atoms within ammonia. Is my interpretation incorrect? I don't think so. Each of the above examples you've cited above is for a C-H bond in an aromatic ring. In OPLS, all N-H bonds involved hydrogen atoms with zero LJ parameters. See, for example, any backbone NH, amide (ASN/GLN), or amine (LYS/LYSH), etc and you will see the atom types used. -Justin Thanks. Darrell Date: Mon, 19 Oct 2009 19:07:22 +1100 From: Mark Abraham Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa To: Discussion list for GROMACS users Message-ID: <4adc1e3a.8010...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Hi, I see that the Lennard Jones parameters for the N & H atoms in ammonia, represented by opls_127 and opls_128 in the file ffoplsaanb.itp are: opls_127 NT 7 14.00670-1.020 A3.42000e-01 7.11280e-01 opls_128 H 1 1.00800 0.340 A0.0e+00 0.0e+00 Why are sigma and epsilon both zero for H? Are the LJ parameters for H embedded in the parameter for NT? If so, how were these parameters combined? What do other H have? What do the OPLS-AA paper(s) have to say about such H atoms? 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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] Lennard Jones Parameters for Ammonia in ffoplsaa
Darrell Koskinen wrote: Hi, I see that the Lennard Jones parameters for the N & H atoms in ammonia, represented by opls_127 and opls_128 in the file ffoplsaanb.itp are: opls_127 NT 7 14.00670-1.020 A3.42000e-01 7.11280e-01 opls_128 H 1 1.00800 0.340 A0.0e+00 0.0e+00 Why are sigma and epsilon both zero for H? Are the LJ parameters for H embedded in the parameter for NT? If so, how were these parameters combined? What do other H have? What do the OPLS-AA paper(s) have to say about such H atoms? 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
