Dear Berk, It looks to me some thing is wrong when i change the radius from 35 to 25, herewith i am giving grpopts for both systems
+++++++++++++++++++++++++ grpopts: (system with 35 A) nrdf: 33141.4 0 ref_t: 300 0 tau_t: 0.1 0.1 +++++++++++++++++++++++++ > grpopts: (system with 25A) > nrdf: 0 0 > ref_t: 300 0 > tau_t: 0.1 0.1 > ++++++++++++++++++++++++ > > I think some thing is going wrong when the size of freezing group is increased. I don't know whether my understand is correct or not. > Thanks > Srinivas. > > > On Fri, Feb 26, 2010 at 11:01 AM, Berk Hess <g...@hotmail.com> wrote: > >> Ah, but that does not correspond to the mdp options tou mailed. >> Here there is only one group with 0 degrees of freedom and reference >> temperature 0. >> >> Berk >> >> ------------------------------ >> Date: Fri, 26 Feb 2010 10:50:13 -0500 >> >> Subject: Re: [gmx-users] problem with the size of freeze groups >> From: jampa...@gmail.com >> To: gmx-users@gromacs.org >> >> HI >> >> Thanks, My log file shows me "nrdf: 0" >> >> ############### >> >> grpopts: >> nrdf: 0 >> ref_t: 0 >> tau_t: 0 >> >> ############### >> >> Thanks >> Srinivas. >> >> On Fri, Feb 26, 2010 at 10:25 AM, Berk Hess <g...@hotmail.com> wrote: >> >> Hi, >> >> Then I have no clue what might be wrong. >> Have you check nrdf in the log file? >> >> Berk >> >> ------------------------------ >> Date: Fri, 26 Feb 2010 09:54:22 -0500 >> Subject: Re: [gmx-users] problem with the size of freeze groups >> >> From: jampa...@gmail.com >> To: gmx-users@gromacs.org >> >> Dear Berk, >> >> Thanks for your response, As you mentioned i have separated t-coupling >> group for frozen and non-frozen groups, still the result is same. >> Herewith i am giving my md.mdp file, Can you suggest me if i am missing >> any options in my md.mdp file? >> >> Thanks again >> Srinivas. >> >> md.mdp file >> >> +++++++++++++++++++++++++++++++++++++++++++++++ >> title = AB2130 >> cpp = /usr/bin/cpp >> constraints = all-bonds >> integrator = md >> dt = 0.002 ; ps ! >> nsteps = 1500000 ; total 3.0 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 = 300 0 >> gen_vel = yes >> gen_temp = 300.0 >> acc_grps = Tmp2 >> accelerate = 0.1 0.1 0.1 >> gen_seed = 173529 >> freezegrps = Tmp2 >> freezedim = Y Y Y >> +++++++++++++++++++++++++++++++++++++++++++++++ >> >> On Fri, Feb 26, 2010 at 6:25 AM, Berk Hess <g...@hotmail.com> wrote: >> >> Hi, >> >> It seems there is a bug in grompp, which subtracts degrees of freedom for >> constraints in water also for frozen water molecules. >> I guess the md.log file reports zero degrees of freedom for your t-coupl >> group. >> You can circumvent this issue by putting all your frozen atoms in a >> separate >> t-coupling group. >> >> Berk >> >> ------------------------------ >> Date: Wed, 24 Feb 2010 21:34:30 -0500 >> From: jampa...@gmail.com >> >> To: gmx-users@gromacs.org >> Subject: [gmx-users] problem with the size of freeze groups >> >> >> Dear Gromacs Users, >> >> I would like to compare the diffusion coefficient of water in different >> confined spheres with the bulk solvent, I have taken a solvent box of size >> 7nm, and I have created a sphere with radius 25 Å as lowest and 35 Å as >> highest spheres. I have not used the pressure coupling for MD, and temp >> coupling is applied for freezing and non freezing waters separately. In case >> of the bigger sphere (i. e, 35 Å) the diffusion coefficient is 2.4 10-5 >> cm2/s (comparable with bulk), but the system with 25 Å radius gives me >> almost 0 diffusion coefficient. When I open the log file of 25 Å system it >> shows the initial temperature as zero. >> >> Is there any relation between size of freezing group and temperature >> coupling? How the sphere with 35 Å radius is working fine but not with the >> radius 25 Å? >> Can anybody help me? >> Here is my m.mdp file >> +++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> title = AB2130 >> cpp = /usr/bin/cpp >> constraints = all-bonds >> integrator = md >> dt = 0.002 ; ps ! >> nsteps = 1500000 ; total 3.0 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 = 300 0 >> gen_vel = yes >> gen_temp = 300.0 >> acc_grps = Tmp2 >> accelerate = 0.1 0.1 0.1 >> gen_seed = 173529 >> freezegrps = Freez >> freezedim = Y Y Y >> +++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> >> -- >> ********************************************* >> J. Srinivasa Rao >> Post-doctoral Research Associate >> Computational Biophysics Group >> Department of Physics >> Drexel University >> 3141 Chestnut St >> Philadelphia, PA 19104 >> Ph: Off: 215-895-1989 >> Mob: 704-706-4191 >> Web:http://jsrao.web.officelive.com/default.aspx >> ********************************************** >> >> >> >> >> ------------------------------ >> Express yourself instantly with MSN Messenger! MSN >> Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> >> >> -- >> 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 >> Ph: Off: 215-895-1989 >> Mob: 704-706-4191 >> Web:http://jsrao.web.officelive.com/default.aspx >> ********************************************** >> >> >> >> ------------------------------ >> New Windows 7: Find the right PC for you. Learn >> more.<http://windows.microsoft.com/shop> >> >> -- >> 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 >> Ph: Off: 215-895-1989 >> Mob: 704-706-4191 >> Web:http://jsrao.web.officelive.com/default.aspx >> ********************************************** >> >> >> >> ------------------------------ >> New Windows 7: Simplify what you do everyday. Find the right PC for >> you.<http://windows.microsoft.com/shop> >> >> -- >> 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 > Ph: Off: 215-895-1989 > Mob: 704-706-4191 > Web:http://jsrao.web.officelive.com/default.aspx > ********************************************** > > > -- ********************************************* 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 Ph: Off: 215-895-1989 Mob: 704-706-4191 Web:http://jsrao.web.officelive.com/default.aspx **********************************************
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