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Hi,<br><br>I think this is a bug in 4.0.3.<br>Please switch to 4.0.4.<br><br>Berk<br><br><br><hr id="stopSpelling">Date: Sat, 4 Apr 2009 22:00:44 +0530<br>From: polley.anirban@gmail.com<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] problem in pulling in gromacs 4.03<br><br>Dear sir,<br> 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.<br>
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.<br>
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.<br> Can you please help me and tell me how to do it? I am eagerly waiting for your help.<br>
<br>;<br> <br>title = lipid bilayer in water<br>cpp = /lib/cpp<br> <br>integrator = sd ; stochastic dynamics -> Langevin!<br>ld_seed = -1 ; random seed for sd <br>
dt = 0.002 ; ps !<br>nsteps = 250000 ; total 500 ps<br>nstcomm = 1 ; freq. for cm-motion removal<br>tinit = 0 ; starting time (ps)<br>
<br>constraints = all-bonds ; constraint for all bond lengths<br>constraint_algorithm = lincs ; default<br>lincs_order = 4 ; default<br> <br>nstxout = 5000 ; T(x_out) 10 ps<br>
nstvout = 5000 ; T(v_out) 10 ps<br>nstfout = 0 ; T(f_out)<br>nstlog = 250 ; energies to log (0.5 ps)<br>nstenergy = 250 ; energies to energy file<br>
<br>ns_type = grid ; nl type<br>nstlist = 10 ; Freq. to update neighbour list<br>rlist = 1.0 ; nm (cutoff for short-range nl)<br> <br>coulombtype = PME ;Reaction-Field ; Coulomb interactions<br>
rcoulomb = 1.0 ;2.0 ; nm (Coulomb cut-off!!)<br>epsilon_r = 80.0 ; dielectric constant for reaction field<br>vdwtype = Cut-off ; Wan der Waals interactions<br>
rvdw = 1.0 ; nm (LJ cut-off)<br>optimize_fft = yes <br><br>; Temperature coupling<br>Tcoupl = no ; no effect when integrator = sd<br>tc-grps = DPP SM CHOL SOL GPI <br>
tau_t = 0.1 0.1 0.1 0.1 0.1<br>ref_t = 310 310 310 310 310<br> <br>; Pressure coupling<br>Pcoupl = no<br>;Pcoupl = berendsen<br>Pcoupltype = semiisotropic<br>
tau_p = 1.0 1.0 ; ps<br>compressibility = 4.5e-5 4.5e-5 ; 1/bar (water: 1 atm, 300 K)<br>ref_p = 1.0 1.0 ; bar<br> <br>; Generate velocites in the beginning<br>gen_vel = yes <br>
gen_temp = 310.0<br>gen_seed = 173529 <br><br><br>;............................................................................................................<br>;pulling<br>pull = umbrella<br>pull_geometry = direction<br>
pull_start = yes<br>pull_ngroups = 1<br>pull_group0 = DPP<br>pull_group1 = GPI <br>pull_dim = N N Y<br>pull_k1 = 100<br>;pull_kB1 = 500<br>pull_rate1 = 0.0005<br>pull_vec1 = 0 0 1<br>pull_init1 = 0.0<br>pull_nstxout = 1 <br>
<br><br>Thanking you,<br>Anirban<br><br /><hr />See all the ways you can stay connected <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>to friends and family</a></body>
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