Re: [gmx-users] TOP file question
Which version of the manual are you using? I recall the discussion on [pairs_nb] being absent in an older version, but manual section 5.3.4 in version 4.6.1 has lots of discussion on [pairs_nb]. I was looking at the 4.5.3 manual. I just downloaded the 4.6.1 manual, and I see it now discusses that option. But here's what it says: The normal pair interactions, intended for 1-4 interactions, have function type 1. Function type 2 and the [ pairs_nb ] are intended for free-energy simulations. So that still leaves my question about Coulomb parameters, since function type 1 doesn't specify them. Peter -- 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] TOP file question
On Fri, Mar 29, 2013 at 1:16 PM, Peter Eastman peast...@stanford.eduwrote: Which version of the manual are you using? I recall the discussion on [pairs_nb] being absent in an older version, but manual section 5.3.4 in version 4.6.1 has lots of discussion on [pairs_nb]. I was looking at the 4.5.3 manual. I just downloaded the 4.6.1 manual, and I see it now discusses that option. But here's what it says: The normal pair interactions, intended for 1-4 interactions, have function type 1. Function type 2 and the [ pairs_nb ] are intended for free-energy simulations. So that still leaves my question about Coulomb parameters, since function type 1 doesn't specify them. Coulombic interactions are always scaled by the value of fudgeQQ (see discussion on [defaults] directive in manual section 5.7.1). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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] TOP file question
Ok, thanks. Peter On Mar 29, 2013, at 10:22 AM, Justin Lemkul jalem...@vt.edu wrote: On Fri, Mar 29, 2013 at 1:16 PM, Peter Eastman peast...@stanford.eduwrote: Which version of the manual are you using? I recall the discussion on [pairs_nb] being absent in an older version, but manual section 5.3.4 in version 4.6.1 has lots of discussion on [pairs_nb]. I was looking at the 4.5.3 manual. I just downloaded the 4.6.1 manual, and I see it now discusses that option. But here's what it says: The normal pair interactions, intended for 1-4 interactions, have function type 1. Function type 2 and the [ pairs_nb ] are intended for free-energy simulations. So that still leaves my question about Coulomb parameters, since function type 1 doesn't specify them. Coulombic interactions are always scaled by the value of fudgeQQ (see discussion on [defaults] directive in manual section 5.7.1). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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] TOP file question
On 3/27/13 5:12 PM, Peter Eastman wrote: I'm implementing a TOP file reader, and I have a question about an ambiguity in the format. The [ pairs ] block lists atom pairs that should be handled specially (exclusions and 1-4 interactions). In addition, the gen-pairs flag can indicate that pairs are generated automatically. But all the files I've looked at include BOTH of these things, and I'm not sure how to interpret that. Can I assume that all pairs generated by gen-pairs are already included in the list, or might I have to generate additional ones? Can I assume that all pairs listed in the file where generated by gen-pairs, or might there be additional pairs that came from somewhere else? What if the two definitions disagree with each other, and the [ pairs ] block lists different parameters for a pair than would be generated automatically? Which should I use? The presence of [pairs] is not dependent upon gen-pairs, but the parameters utilized by those pairs are. All force fields deal with 1-4 interactions in some way, but the manner in which they do so is different. For instance, in Gromos96 parameter sets, the gen-pairs keyword is set to no, and all pair interactions are looked up from the [pairtypes] directive in ffnonbonded.itp, whereas for other force fields (OPLS, AMBER), the pair interactions are simply calculated according to normal combination rules with fudge factors (i.e., gen-pairs set to yes). CHARMM uses a hybrid approach wherein some pairs are set in [pairtypes], but anything not listed there is generated. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] TOP file question
Hi Justin, So if I understand you correctly, there are actually three different ways the parameters can be specified. In order of decreasing precedence: 1. If there's a [pairs] line and it includes parameters, use those parameters. 2. If there's a [pairs] line and it doesn't include parameters, look for a corresponding [pairtypes] lines and, if we find one, use that. 3. If gen-pairs is yes, then generate parameters for all 1-2, 1-3, and 1-4 pairs for which we did not already find parameters in step 1 or 2 (regardless of whether or not a [pairs] line exists for a particular pair). Is that correct? Thanks! Peter On Mar 28, 2013, at 4:20 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/27/13 5:12 PM, Peter Eastman wrote: I'm implementing a TOP file reader, and I have a question about an ambiguity in the format. The [ pairs ] block lists atom pairs that should be handled specially (exclusions and 1-4 interactions). In addition, the gen-pairs flag can indicate that pairs are generated automatically. But all the files I've looked at include BOTH of these things, and I'm not sure how to interpret that. Can I assume that all pairs generated by gen-pairs are already included in the list, or might I have to generate additional ones? Can I assume that all pairs listed in the file where generated by gen-pairs, or might there be additional pairs that came from somewhere else? What if the two definitions disagree with each other, and the [ pairs ] block lists different parameters for a pair than would be generated automatically? Which should I use? The presence of [pairs] is not dependent upon gen-pairs, but the parameters utilized by those pairs are. All force fields deal with 1-4 interactions in some way, but the manner in which they do so is different. For instance, in Gromos96 parameter sets, the gen-pairs keyword is set to no, and all pair interactions are looked up from the [pairtypes] directive in ffnonbonded.itp, whereas for other force fields (OPLS, AMBER), the pair interactions are simply calculated according to normal combination rules with fudge factors (i.e., gen-pairs set to yes). CHARMM uses a hybrid approach wherein some pairs are set in [pairtypes], but anything not listed there is generated. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] TOP file question
3. If gen-pairs is yes, then generate parameters for all 1-2, 1-3, and 1-4 pairs for which we did not already find parameters in step 1 or 2 (regardless of whether or not a [pairs] line exists for a particular pair). Or rather, generate an [exclusions] record for each 1-2 and 1-3, and a [pairs] record for each 1-4. Peter-- 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] TOP file question
After further study of the documentation, I find myself getting more confused rather than less. I see that the [pairs] and [pairtypes] directives only specify LJ parameters, not Coulomb parameters. (There's a function type 2 for [pairs] that does include charges, but the manual says that function type is only used for free energy calculations.) How do I select the latter when gen-pairs is off? Is it simply assumed that 1-4 Coulomb interactions are never reduced for force fields that don't use gen-pairs? Table 5.5 lists an alternate directive, [pairs_nb] that does specify Coulomb parameters as well as LJ. But no other mention of this directive appears anywhere else in the manual, there doesn't seem to be any corresponding [pairtypes] option, and a grep reveals that pairs_nb never occurs in any file in the entire top directory. What am I misunderstanding? Peter-- 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] TOP file question
On 3/28/13 7:14 PM, Peter Eastman wrote: 3. If gen-pairs is yes, then generate parameters for all 1-2, 1-3, and 1-4 pairs for which we did not already find parameters in step 1 or 2 (regardless of whether or not a [pairs] line exists for a particular pair). Or rather, generate an [exclusions] record for each 1-2 and 1-3, and a [pairs] record for each 1-4. Not quite. The presence of an entry in [pairs] is required. When processing the topology, grompp doesn't do any magic. It won't generate pair interactions for any combination for which there is no entry. I think gen-pairs is somewhat misleading. It doesn't generate pairs. It generates parameters for the pairs that the user (or pdb2gmx/g_x2top) has listed, which assumes proper use of the force field. For a bit more discussion of how this all works: http://lists.gromacs.org/pipermail/gmx-users/2012-December/077005.html -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] TOP file question
On 3/28/13 8:25 PM, Peter Eastman wrote: After further study of the documentation, I find myself getting more confused rather than less. I see that the [pairs] and [pairtypes] directives only specify LJ parameters, not Coulomb parameters. (There's a function type 2 for [pairs] that does include charges, but the manual says that function type is only used for free energy calculations.) How do I select the latter when gen-pairs is off? Is it simply assumed that 1-4 Coulomb interactions are never reduced for force fields that don't use gen-pairs? Table 5.5 lists an alternate directive, [pairs_nb] that does specify Coulomb parameters as well as LJ. But no other mention of this directive appears anywhere else in the manual, there doesn't seem to be any corresponding [pairtypes] option, and a grep reveals that pairs_nb never occurs in any file in the entire top directory. What am I misunderstanding? Which version of the manual are you using? I recall the discussion on [pairs_nb] being absent in an older version, but manual section 5.3.4 in version 4.6.1 has lots of discussion on [pairs_nb]. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] TOP file question
I'm implementing a TOP file reader, and I have a question about an ambiguity in the format. The [ pairs ] block lists atom pairs that should be handled specially (exclusions and 1-4 interactions). In addition, the gen-pairs flag can indicate that pairs are generated automatically. But all the files I've looked at include BOTH of these things, and I'm not sure how to interpret that. Can I assume that all pairs generated by gen-pairs are already included in the list, or might I have to generate additional ones? Can I assume that all pairs listed in the file where generated by gen-pairs, or might there be additional pairs that came from somewhere else? What if the two definitions disagree with each other, and the [ pairs ] block lists different parameters for a pair than would be generated automatically? Which should I use? Thanks. Peter-- 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
