[gmx-users] Re: Free Energy Calculations in Gromacs
Thanks Justin and Professor Shirts. The gmxdump on the resulting tpr did indeed solve a lot of my problems. Thanks again. -- View this message in context: http://gromacs.5086.x6.nabble.com/Free-Energy-Calculations-in-Gromacs-tp5007495p5009115.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: Free Energy Calculations in Gromacs
Hi, I have been trying to perform the simulations using the amber forcefield, in which the [ pairtypes ] directive is not defined explicitly in the ffnonbonded.itp file, but rather the 1-4 interactions are generated as per the defaults section in the forcefield.itp file. I was wondering what happens to these 1-4 interactions at lambda=1 state? Suppose 1 corresponds to CA and 4 corresponds to NA at state A (lambda = 0) and the CA_per and NA_per are the corresponding atomtypes at state B (lambda = 1). It is defined in the topology file that ... ... [ pairs ] 1 4 1 So does it mean that at state B (lambda = 1), the 1-4 nonbonded interactions will be calculated between CA_per and NA_per? Although the [ pairs_nb ] section is described in the manual, I would appreciate if someone elaborates a little more. -- View this message in context: http://gromacs.5086.x6.nabble.com/Free-Energy-Calculations-in-Gromacs-tp5007495p5008996.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: Free Energy Calculations in Gromacs
On 6/10/13 2:50 PM, JW Gibbs wrote: Hi, I have been trying to perform the simulations using the amber forcefield, in which the [ pairtypes ] directive is not defined explicitly in the ffnonbonded.itp file, but rather the 1-4 interactions are generated as per the defaults section in the forcefield.itp file. I was wondering what happens to these 1-4 interactions at lambda=1 state? Suppose 1 corresponds to CA and 4 corresponds to NA at state A (lambda = 0) and the CA_per and NA_per are the corresponding atomtypes at state B (lambda = 1). It is defined in the topology file that ... ... [ pairs ] 1 4 1 So does it mean that at state B (lambda = 1), the 1-4 nonbonded interactions will be calculated between CA_per and NA_per? Although the [ pairs_nb ] section is described in the manual, I would appreciate if someone elaborates a little more. The actual answer depends on exactly how you're treating the system. Are you using [pairs_nb] in your topology or just [pairs]? The outcome will be different depending on which you're using. Also note that, as the manual says, you don't really need to mess with [pairs_nb] at all; you can achieve unscaled internal interactions using couple-intramol = no in the .mdp file. Without seeing the .mdp file, it's even more difficult to know what you're doing and what you should expect. -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] Re: Free Energy Calculations in Gromacs
An important final point is that you can always see EXACTLY what grompp is putting into the B state by running gmxdump on the resulting tpr. It's a LOT of information, but all in text all the interactions are listed explicitly there. On Mon, Jun 10, 2013 at 6:20 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 2:50 PM, JW Gibbs wrote: Hi, I have been trying to perform the simulations using the amber forcefield, in which the [ pairtypes ] directive is not defined explicitly in the ffnonbonded.itp file, but rather the 1-4 interactions are generated as per the defaults section in the forcefield.itp file. I was wondering what happens to these 1-4 interactions at lambda=1 state? Suppose 1 corresponds to CA and 4 corresponds to NA at state A (lambda = 0) and the CA_per and NA_per are the corresponding atomtypes at state B (lambda = 1). It is defined in the topology file that ... ... [ pairs ] 1 4 1 So does it mean that at state B (lambda = 1), the 1-4 nonbonded interactions will be calculated between CA_per and NA_per? Although the [ pairs_nb ] section is described in the manual, I would appreciate if someone elaborates a little more. The actual answer depends on exactly how you're treating the system. Are you using [pairs_nb] in your topology or just [pairs]? The outcome will be different depending on which you're using. Also note that, as the manual says, you don't really need to mess with [pairs_nb] at all; you can achieve unscaled internal interactions using couple-intramol = no in the .mdp file. Without seeing the .mdp file, it's even more difficult to know what you're doing and what you should expect. -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
