Other then to use 4.0.4, i would try to change the simulation-time, the force-constant of the spring (pull_k1) and the pulling velocity (pull_rate1). You have both a low force-constant and a slow pulling velocity, with a simulation-time around 500ps it is possible that only see the protein vibrating, because it needs more time. So best would probably to increase 'pull_k1' and 'pull_rate1' and simulate longer.
Thomas > > > Hi, > > I think this is a bug in 4.0.3. > Please switch to 4.0.4. > > Berk > > > Date: Sat, 4 Apr 2009 22:00:44 +0530 > From: polley.anir...@gmail.com > To: gmx-users@gromacs.org > Subject: [gmx-users] problem in pulling in gromacs 4.03 > > Dear sir, > I want to pull a small protein molecule (GPI) which is inserted > on the upper layer of the bilayer. So, I applied pull = umbrella, where > umbrella potential is used between center of mass of reference group and that > of pulled group. Now, as I want to pull the protein from the lipid bilayer > membrane, I use the whole molecule of protein as pulled group and the whole > patch of bilayer as a reference group because I thought that though I write > the whole patch of bilayer as a reference group, the pull will occur w.r.t. > the center of mass of the reference group. It will create no problem. > Similarly, I did for the whole protein as a pulled group. > > I tried the pull_geometry as all distance, direction, position > and it does not give any error during simulation. But, when I saw the whole > trajectory in VMD, then I saw that the protein did not come out by the > pulling. It is just vibrating at the same position. > > When I ran the simulation in NVT ensemble, the bilayer still > retain its structure but when I ran it in NPT ensemble, it created crazy > things, water entered inside, lipids became shrinked and so on. > Can you please help me and tell me how to do it? I am eagerly > waiting for your help. > > > ; > > title = lipid bilayer in water > cpp = /lib/cpp > > integrator = sd ; stochastic dynamics -> Langevin! > ld_seed = -1 ; random seed for sd > > dt = 0.002 ; ps ! > nsteps = 250000 ; total 500 ps > nstcomm = 1 ; freq. for cm-motion removal > tinit = 0 ; starting time (ps) > > > constraints = all-bonds ; constraint for all bond lengths > constraint_algorithm = lincs ; default > lincs_order = 4 ; default > > nstxout = 5000 ; T(x_out) 10 ps > > nstvout = 5000 ; T(v_out) 10 ps > nstfout = 0 ; T(f_out) > nstlog = 250 ; energies to log (0.5 ps) > nstenergy = 250 ; energies to energy file > > > ns_type = grid ; nl type > nstlist = 10 ; Freq. to update neighbour list > rlist = 1.0 ; nm (cutoff for short-range nl) > > coulombtype = PME ;Reaction-Field ; Coulomb > interactions > > rcoulomb = 1.0 ;2.0 ; nm (Coulomb > cut-off!!) > epsilon_r = 80.0 ; dielectric constant for reaction > field > vdwtype = Cut-off ; Wan der Waals interactions > > rvdw = 1.0 ; nm (LJ cut-off) > optimize_fft = yes > > ; Temperature coupling > Tcoupl = no ; no effect when integrator = sd > tc-grps = DPP SM CHOL SOL GPI > > tau_t = 0.1 0.1 0.1 0.1 0.1 > ref_t = 310 310 310 310 310 > > ; Pressure coupling > Pcoupl = no > ;Pcoupl = berendsen > Pcoupltype = semiisotropic > > tau_p = 1.0 1.0 ; ps > compressibility = 4.5e-5 4.5e-5 ; 1/bar (water: 1 atm, 300 K) > ref_p = 1.0 1.0 ; bar > > ; Generate velocites in the beginning > gen_vel = yes > > gen_temp = 310.0 > gen_seed = 173529 > > > ;............................................................................................................ > ;pulling > pull = umbrella > pull_geometry = direction > > pull_start = yes > pull_ngroups = 1 > pull_group0 = DPP > pull_group1 = GPI > pull_dim = N N Y > pull_k1 = 100 > ;pull_kB1 = 500 > pull_rate1 = 0.0005 > pull_vec1 = 0 0 1 > pull_init1 = 0.0 > pull_nstxout = 1 > > > > Thanking you, > Anirban > > _________________________________________________________________ > See all the ways you can stay connected to friends and family > http://www.microsoft.com/windows/windowslive/default.aspx > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090405/8b874d63/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Sun, 5 Apr 2009 20:47:19 +0800 > From: friendli <friendli2...@gmail.com> > Subject: [gmx-users] dgdl convergence in free energy calculation > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <43db0a8a0904050547i5a55820eodc7275b2b027f...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Skipped content of type multipart/alternative-------------- next part > -------------- > A non-text attachment was scrubbed... > Name: dgdl.jpg > Type: image/jpeg > Size: 32729 bytes > Desc: not available > Url : > http://www.gromacs.org/pipermail/gmx-users/attachments/20090405/b071a0db/dgdl.jpg > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 60, Issue 31 > ***************************************** _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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