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 **********************************************
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