[gmx-users] Thole Potential
Hi, I am trying to use Thole potential to implement polarization effects with drudes. I know NAMD and CHARMM have clear protocols, but I am unable to find much information on how it is implemented in Gromacs. Can someone tell me where I can find an example file to understand the use of [polarization] and [thole_polarization] in the topology file? Thanks, Sai -- *"Every sentence I utter must be understood not as an affirmation but as a question." - Niels Bohr* -- 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] (no subject)
Oh, thanks! On Thu, Oct 6, 2011 at 7:59 PM, Justin A. Lemkul wrote: > > > Sai Janani Ganesan wrote: > >> Hi, >> >> Thanks for the reply! >> >> I tried the rates, and only the terminal with positive rate gets pulled. >> >> The first and the last amino acids are spatially oriented one behind the >> other. I think defining a vector might work better, but I am not sure why >> nothing happens when I define a pull_vec1 and pull_vec2. Am I missing >> anything? >> >> > When setting "distance" as the pull_geometry, only pull_dim is used; > pull_vec is ignored. If you want to define vectors, use the "direction" > pull_geometry. > > -Justin > > Thanks, >> Sai >> >> >> >> >> On Thu, Oct 6, 2011 at 9:14 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Sai Janani Ganesan wrote: >> >>Hi, >> >>I am trying to pull the first from the last amino acid of a >>protein to completely unfold the protein in the X direction. I >>chose the middle amino acid as the reference, and the groups get >>pulled in the same direction or opposite direction (which is >>what I want) depending on the trial. I am trying to find a >>definite method to completely unfold it. >>I define a different vector (pull_vec1 and pull_vec2) with +x >>and -x values and that does not even pull the protein >>I tried using only pull_group1 and pull_group2, without a >>reference, and neither groups get pulled. >>I chose different references, I do have some success but I don't >>think it is the best way to do it. >> >>How do I pull the N and C terminal apart, by simultaneously >>pulling them in opposite directions?Why is my vector definition >>wrong? >> >>This is my pull code: >> >>pull= umbrella >>pull_geometry = distance >>pull_dim= Y N N >>pull_start = yes pull_ngroups= 2 >>pull_group0 = Chain-C >>pull_group1 = Chain-B >>pull_group2 = Chain-A >> >>%pull_vec1 = -31 0 0 >>%pull_vec2 = 31 0 0 >> >> >>I suspect the % signs will mess things up, but probably will give a >>fatal error, if nothing else. >> >> >>pull_rate1 = 0.002pull_k1 = 1000pull_rate2 >> = 0.002 pull_k2 = 1000 >> >>Here's the problem. You're telling the two pulled groups to move in >>the same direction. With "distance" geometry, the selections are a >>bit more simplistic. If you set pull_rate1 to -0.002 and pull_rate2 >>to 0.002, the groups will be pulled in opposite directions. >> Otherwise, you're just towing your protein along in the box. >> >>-Justin >> >>-- ==**__== >> >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>MILES-IGERT Trainee >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> > >> >>==**__== >> >>-- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >>Please search the archive at >> >> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Search<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 >><mailto:gmx-users-requ
Re: [gmx-users] (no subject)
Hi, Thanks for the reply! I tried the rates, and only the terminal with positive rate gets pulled. The first and the last amino acids are spatially oriented one behind the other. I think defining a vector might work better, but I am not sure why nothing happens when I define a pull_vec1 and pull_vec2. Am I missing anything? Thanks, Sai On Thu, Oct 6, 2011 at 9:14 AM, Justin A. Lemkul wrote: > > > Sai Janani Ganesan wrote: > >> Hi, >> >> I am trying to pull the first from the last amino acid of a protein to >> completely unfold the protein in the X direction. I chose the middle amino >> acid as the reference, and the groups get pulled in the same direction or >> opposite direction (which is what I want) depending on the trial. I am >> trying to find a definite method to completely unfold it. >> I define a different vector (pull_vec1 and pull_vec2) with +x and -x >> values and that does not even pull the protein >> I tried using only pull_group1 and pull_group2, without a reference, and >> neither groups get pulled. >> I chose different references, I do have some success but I don't think it >> is the best way to do it. >> >> How do I pull the N and C terminal apart, by simultaneously pulling them >> in opposite directions?Why is my vector definition wrong? >> >> This is my pull code: >> >> pull= umbrella >> pull_geometry = distance >> pull_dim= Y N N >> pull_start = yes pull_ngroups= 2 >> pull_group0 = Chain-C >> pull_group1 = Chain-B >> pull_group2 = Chain-A >> >> %pull_vec1 = -31 0 0 >> %pull_vec2 = 31 0 0 >> > > I suspect the % signs will mess things up, but probably will give a fatal > error, if nothing else. > > > pull_rate1 = 0.002pull_k1 = 1000pull_rate2 = >> 0.002 pull_k2 = 1000 >> > > Here's the problem. You're telling the two pulled groups to move in the > same direction. With "distance" geometry, the selections are a bit more > simplistic. If you set pull_rate1 to -0.002 and pull_rate2 to 0.002, the > groups will be pulled in opposite directions. Otherwise, you're just towing > your protein along in the box. > > -Justin > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- *"Every sentence I utter must be understood not as an affirmation but as a question." - Niels Bohr* -- 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] (no subject)
Hi, I am trying to pull the first from the last amino acid of a protein to completely unfold the protein in the X direction. I chose the middle amino acid as the reference, and the groups get pulled in the same direction or opposite direction (which is what I want) depending on the trial. I am trying to find a definite method to completely unfold it. I define a different vector (pull_vec1 and pull_vec2) with +x and -x values and that does not even pull the protein I tried using only pull_group1 and pull_group2, without a reference, and neither groups get pulled. I chose different references, I do have some success but I don't think it is the best way to do it. How do I pull the N and C terminal apart, by simultaneously pulling them in opposite directions?Why is my vector definition wrong? This is my pull code: pull= umbrella pull_geometry = distance pull_dim= Y N N pull_start = yes pull_ngroups= 2 pull_group0 = Chain-C pull_group1 = Chain-B pull_group2 = Chain-A %pull_vec1 = -31 0 0 %pull_vec2 = 31 0 0 pull_rate1 = 0.002 pull_k1 = 1000 pull_rate2 = 0.002 pull_k2 = 1000 Thanks! -- *"Every sentence I utter must be understood not as an affirmation but as a question." - Niels Bohr* -- 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
