Dear Justin, Thanks for your responce. Here is my mdp file.
+++++++++++++++++++++++++++++++++++++++ title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.004 ; ps ! nsteps = 25000000 ; total 100.0 ns. nstcomm = 1 nstxout = 1000 ; collect data every 2.0 ps nstvout = 1000 ; collect velocity every 2.0 ps nstfout = 0 nstlog = 0 nstenergy = 1000 ; collect energy every 2.0 ps nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 rvdw_switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tau_t = 0.1 0.1 tc-grps = Tmp1 Tmp2 ref_t = 283.0 0.0 gen_vel = yes gen_temp = 283.0 acc_grps = Tmp1 accelerate = 0.1 0.1 0.1 gen_seed = 181726 freezegrps = Tmp2 freezedim = Y Y Y ++++++++++++++++++++++++++++++++++++++++++++++++ Thanks Srinivas. On Thu, Apr 8, 2010 at 7:52 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > jampani srinivas wrote: > >> Hi >> Thanks for your response, I am allowing the two groups (frozen and >> non-frozen) groups interact each other, i guess i am getting the energy of >> total system from g_energy. >> I checked the velocities of frozen group atoms, they are not "zero". I >> have seen in git master that this problem was fixed and updated in md.c >> file, I have downloaded this from git master and compiled my gromacs again >> still i found that frozen atoms gets the initial velocity. >> I am not at all clear why the energy of system should blow up, can you >> please help me if there is solution for this. >> >> > > I haven't been following this closely; can you post an .mdp file? > > -Justin > > Thanks in advance. >> Srinivas. >> >> >> On Wed, Apr 7, 2010 at 4:47 PM, ms <deviceran...@gmail.com <mailto: >> deviceran...@gmail.com>> wrote: >> >> jampani srinivas ha scritto: >> > Dear Berk, >> > >> > I am sorry if i am confusing you with my poor description of >> problem, >> > actually I have submitted simulation with two temperature >> coupling groups (i >> > think you already know that from our earlier conversations) and >> found that >> > there is a continuous increase in the total energy of the system. >> I could >> > not observe any blowing in the output file but the system energy is >> > continuously increasing, i am using 4fs time step here. Can you >> please let >> > me know if i have to give more details? >> > >> >> Which part of the system is increasing its energy? >> >> m. >> -- >> 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/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/mailing_lists/users.php >> >> >> >> >> -- >> ********************************************* >> J. Srinivasa Rao >> Post-doctoral Research Associate >> C/o Prof. Luis R Cruz Cruz >> Computational Biophysics Group >> Department of Physics >> Drexel University >> 3141 Chestnut St >> Philadelphia, PA 19104, USA. >> Ph: Off: 215-895-1989 >> Mob: 704-706-4191 >> Web:http://jsrao.web.officelive.com/default.aspx >> ********************************************** >> >> >> > -- > ======================================== > > 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/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 > -- ********************************************* J. Srinivasa Rao Post-doctoral Research Associate C/o Prof. Luis R Cruz Cruz Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104, USA. Ph: Off: 215-895-1989 Mob: 704-706-4191 Web:http://jsrao.web.officelive.com/default.aspx **********************************************
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