Hi Berk, I am extremely sorry, here is the correct log file
++++++++++++++++ grpopts: nrdf: 0 0 ref_t: 300 0 tau_t: 0.1 0.1 ++++++++++++++++ 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 **********************************************
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