Dear Justin,
I am sorry for the poor description of the problem, OK let me explain you clearly here. I have taken a decapeptide and solvated it with box size 6.0 nm, I want to create a frozen wall (confined sphere) around protein after a certain radius (in this case it is 2.5 nm). To achieve this i made two temperature coupling groups, first (Tmp1) one has protein and waters within 2.5nm from the center of the box and rest is second temperature coupling group (Tmp2). Initially when i run the simulation it was creating nrdf = 0 for both groups, Berk has helped me with a file readir.c file, i compiled my gromacs again that problem was solved. I have submitted simulations again and found that the energy was blowing up. I think you know the story after this. Earlier I want protein to interact with inner wall of the frozen group and check what happens, because of this I have never looked at the energygrps_excl option. I have done with both 2 and 4 fs time steps and I took 4fs option to speed up the simulation, and I have to still look at the paper you suggested me. Thanks for your suggestions, I have implemented your suggestion one after the other, finally when i use the energygrps_excl option it worked out. Now there is no sudden drift in the energy, and also i checked the velocities of non-frozen group is mostly zero (except for first frame) When I use the energygrps_excel option in the following way i am getting the below mentioned note i have to still understand what is this message. On the other hand if i use only "energygrp_excl = Tmp2 Tmp2 Tmp2 Tmp1" line in mdp file i am getting fatal error. Is it necessary to to define the energy groups first and later exclude the energy option? +++++++++++++++++++++++++++++ energygrps = Tmp1 Tmp2 energygrp_excl = Tmp2 Tmp2 Tmp2 Tmp1 ++++++++++++++++++++++++++++++++ NOTE "Can not exclude the lattice Coulomb energy between energy groups" I used -maxwarn option here and generated the tpr file. I hope this does not harm the simulation. Please let me know your comments and suggestion. Thanks very much for your kind help. Srinivas. On Thu, Apr 8, 2010 at 8:21 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > jampani srinivas wrote: > >> 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 >> ++++++++++++++++++++++++++++++++++++++++++++++++ >> > > There are a whole host of reasons that you're seeing an energy drift. > Perhaps you should give a more detailed description of what you're trying > to do. Per your original message, you imply that you have a very simple > system of some frozen and non-frozen group, which is clearly oversimplified. > A few thoughts: > > 1. You're applying constant acceleration, so you're introducing > non-equilibrium conditions. What is Tmp1? Could it be working against Tmp2 > (frozen) in some way that is causing a clash? > > 2. You're not using energrygrp_excl for your frozen group. Per the manual: > > "To avoid spurious contributions to the virial and pressure due to large > forces between completely frozen atoms you need to use energy group > exclusions, this also saves computing time." > > 3. Are you using virtual sites in addition to constraints? Does a shorter > timestep alleviate the energy drift? Have a look at the Gromacs 4 paper for > notes about use of virtual sites and constraints, and the effect on what's > reasonable for the time step. > > I'd suggest working through this systematically - you've got a ton of > variables that could be opposing one another. Introduce them one at a time > to see where your system starts to break down. > > -Justin > > Thanks >> Srinivas. >> >> On Thu, Apr 8, 2010 at 7:52 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> 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> <mailto: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> >> <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/searchbefore >> 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/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 <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/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 **********************************************
-- 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
