Regarding my previous question. I performed 2 simulations (minimization, NVT, NPT, and that 10ns production run), one with 300K and another with 309K. Fir each temperature I calculated how many contacts has my molecule with water within a certain distance. But the number of contacts at different temperatures is the same. It differs on 0.1. I think it has something to do with pressure. I would really like to be able to perform simulations that I could get correct different value of number of contacts versus temperature.
Please could you advice me on this? best, Olga 2011/2/23 Justin A. Lemkul <jalem...@vt.edu> > > > Olga Ivchenko wrote: > >> Yes, I want to plot number of contacts agains tempreture. But in >> thermodynamics when temperature changes the pressure changes or the volume. >> But in my system volume and pressure is the same at different tempretures. >> Just I wanted ti be sure if it is ok to do like this even if the pressure is >> the same at different tempretures. >> >> > I guess this all depends on how "different" your temperatures are. If the > pressures do not change substantially, then there is no problem, since the > system density is reasonably similar. > > -Justin > > best, >> Olga >> >> 2011/2/23 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>> >> >> >> >> >> Olga Ivchenko wrote: >> >> If I am using g_mindist to calculate the number of contacts at >> different tempretures of the system. I am thinking if it will >> make sense because the system has a periodic boundary conditions >> and the pressure at each tempreture is defined manually and is >> the same. The only parameter in the script which should be >> different at different tempretures is pressure. Please could you >> advice me on this? >> >> >> So you want to plot contacts as a function of temperature? I don't >> see any problem with doing that. On what do you need advice? >> >> -Justin >> >> best, >> Olga >> >> 2011/2/21 Justin A. Lemkul <jalem...@vt.edu >> <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu >> <mailto:jalem...@vt.edu>>> >> >> >> >> Olga Ivchenko wrote: >> >> So I used mindist for a certain group of molecules which is >> surrounded by water. I got plot number of contacts versuc >> sumulation time. According to what I see in a distance < >> 0.6nm >> at certain frame there are on average 150 contacts. >> >> Actually how the programm calculates the number of >> contacts, if >> someone knows what is a creteria that a certain contact >> is formed? >> Is is a certain distance. >> >> >> Exactly as the title of the output says, a contact exists if >> any two >> atoms of the chosen index groups are within 0.6 nm. You can >> change >> the distance with g_mindist -d. >> >> -Justin >> >> best, >> Olga >> >> 2011/2/21 Olga Ivchenko <olga.ivche...@gmail.com >> <mailto:olga.ivche...@gmail.com> >> <mailto:olga.ivche...@gmail.com >> <mailto:olga.ivche...@gmail.com>> >> <mailto:olga.ivche...@gmail.com <mailto:olga.ivche...@gmail.com> >> >> <mailto:olga.ivche...@gmail.com >> <mailto:olga.ivche...@gmail.com>>>> >> >> >> Thank you very much. >> best, >> Olga >> >> 2011/2/21 Justin A. Lemkul <jalem...@vt.edu >> <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> >> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> >> >> >> >> >> g_mindist -on (with suitable index groups) should >> also do >> the trick. >> >> -Justin >> >> >> Erik Marklund wrote: >> >> Or g_hbond -contact. Undfortuntely there are >> still issues >> with g_hbond at the moment. Version 4.0.x seem to >> work better. >> >> XAvier Periole skrev 2011-02-21 11.37: >> >> g_dist >> On Feb 21, 2011, at 11:32 AM, Olga >> Ivchenko wrote: >> >> Dear Gromacs Users, >> >> I would like to know if there is in >> gromacs an >> option how to calculate how many >> contacts has a >> certain atom i(n a molecules of interest) >> with water >> during the whole MD simulations (or at >> each >> step of MD). >> Please could you advice me on this? >> >> best, >> Olga >> >> -- gmx-users >> mailing list >> gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> <mailto:gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org >> <mailto:gmx-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 >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>>. >> >> Can't post? Read >> >> http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> >> -- ======================================== >> >> 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> <http://vt.edu> >> <http://vt.edu> | >> >> (540) 231-9080 >> >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> >> -- gmx-users mailing list >> gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> <mailto:gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org >> <mailto:gmx-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 <mailto: >> gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>>. >> >> Can't post? Read >> http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- ======================================== >> >> 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> <http://vt.edu> | (540) >> 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-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 >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> -- ======================================== >> >> 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 >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > 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 > > ======================================== > -- > gmx-users mailing list gmx-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 >
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