<br>
Hi Taveechai,<br>
<br>
Try centering your K at the center of the box rather than the origin. And read a bit on periodic boundary conditions.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br><br><div><span class="gmail_quote">On 9/9/05, <b class="gmail_sendername">taveechai taveecharoenkool</b> <<a href="mailto:taweehui@yahoo.com">taweehui@yahoo.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
dear all,<br> i have a system of six protein-monomers in popc<br>bilayers, there is a pore inside this hexamers. i want<br>to study the free energy difference of K in the pore<br>between mutant and wild-type of this hexamer. i put K
<br>at center of the pore 0 0 0. Then , perform energy<br>minimization by steepest descent, and cg. However,<br>after energy minimization , the system is bigger , the<br>box vector the same . Then i look at the structure by
<br>RasMol the system looks weird. the pore doesn't appear<br>, the proteins went to the corners of the box,<br>bilayers of popc also disappear, water in the middle<br>of popc layer. i remove pbc out using ' editconf -pbc
<br>' , but the system still look the same.<br>please help me , i just want to get K ion in the local<br>minimum of this pore.<br> system size : 13.360 16.203 14.029 (nm)<br> center : 5.301 5.903 5.029 (nm)<br>
box vectors : 10.803 11.910 11.177 (nm)<br>this is mdp file:<br>; VARIOUS PREPROCESSING OPTIONS =<br>title =<br>cpp =
/lib/cpp<br>include =<br>define =<br><br>; RUN CONTROL PARAMETERS =<br>integrator = steep<br>; start time and timestep in ps =<br>tinit = 0<br>dt
= 0.0002<br>nsteps = 50000<br>; =
100 ps REMARK<br>; number of steps for center of mass motion removal =<br>nstcomm = 1<br><br>; LANGEVIN DYNAMICS OPTIONS =<br>; Temperature, friction coefficient (amu/ps) and<br>random seed =<br>bd-temp = 300
<br>bd-fric = 0<br>ld-seed = 1993<br><br>; ENERGY MINIMIZATION OPTIONS =<br>; Force tolerance and initial step-size =<br>emtol = 1<br>emstep = 0.01<br>
; Max number of iterations in relax_shells =<br>niter = 0<br>; Frequency of steepest descents steps when doing CG =<br><br>nstcgsteep = 1000<br>; OUTPUT CONTROL OPTIONS =<br>; Output frequency for coords (x), velocities (v) and
<br>forces (f) =<br>nstxout = 1000<br>nstvout = 1000<br>nstfout = 0<br>; Output frequency for energies to log file and energy<br>file =<br>nstlog = 1000
<br>nstenergy = 1000<br>; Output frequency and precision for xtc file =<br>nstxtcout = 1000<br>xtc-precision = 1000<br>; This selects the subset of atoms for the xtc file.<br>You can =
<br>; select multiple groups. By default all atoms will be<br>written. =<br>xtc-grps =<br>; Selection of energy groups =<br>energygrps = Protein POPC SOL K<br><br>; NEIGHBORSEARCHING PARAMETERS =
<br>; nblist update frequency =<br>nstlist = 15<br>; ns algorithm (simple or grid) =<br>ns-type = Grid<br>; Box type, rectangular, triclinic, none =<br>pbc =
xyz<br>; nblist cut-off =<br>rlist =
1.0<br>domain-decomposition = no<br> OPTIONS FOR ELECTROSTATICS AND VDW =<br>; Method for doing electrostatics =<br>coulombtype = PME<br>rcoulomb-switch = 0<br>rcoulomb = 1.0<br>
; Dielectric constant (DC) for cut-off or DC of<br>reaction field =<br>epsilon-r = 1<br>; Method for doing Van der Waals =<br>vdw-type = Cut-off<br>; cut-off lengths =<br>rvdw-switch = 0
<br>rvdw
= 1.0<br>; Spacing for the PME/PPPM FFT grid =<br>fourierspacing = 0.15<br>; FFT grid size, when a value is 0 fourierspacing will<br>be used =<br>fourier_nx = 0<br>fourier_ny = 0<br>
fourier_nz = 0<br>; EWALD/PME/PPPM parameters =<br>pme_order = 4<br>ewald_rtol = 1e-05<br>optimize_fft = yes<br><br>; OPTIONS FOR WEAK COUPLING ALGORITHMS =<br>; Temperature coupling =
<br>tcoupl = yes<br>; Groups to couple separately =<br>tc-grps =
Protein POPC SOL K<br>tau-t =
0.1 0.1 0.1 0.1<br>ref-t = 300
300 300 300<br>; Pressure coupling =<br>Pcoupl = berendsen<br>Pcoupltype = Anisotropic<br>; Time constant (ps), compressibility (1/bar) and<br>reference P (bar) =<br>tau-p =
1.0<br>compressibility = 4.5E-5 4.5E-5 4.5E-5 4.5E-5<br>4.5E-5 4.5E-5<br>ref-p =
1.0 1.0 1.0 1.0 1.0 1.0<br><br>; SIMULATED ANNEALING CONTROL =<br>; annealing = no<br>; Time at which temperature should be zero (ps) =<br>; zero-temp_time = 0<br><br>; GENERATE VELOCITIES FOR STARTUP RUN =
<br>gen-vel = yes<br>gen-temp = 300<br>gen-seed = 173529<br><br>; OPTIONS FOR BONDS =<br>constraints = all-bonds<br>; Type of constraint algorithm =<br>constraint-algorithm = Lincs
<br>; Do not constrain the start configuration =<br>unconstrained-start = no<br>; Relative tolerance of shake =<br>shake-tol = 0.0001<br>; Highest order in the expansion of the constraint<br>coupling matrix =
<br>lincs-order = 4<br>; Lincs will write a warning to the stderr if in one<br>step a bond =<br>;rotates over more degrees than =<br><br> lincs-warnangle = 30<br>; Convert harmonic bonds to morse potentials =
<br>morse =
no<br><br>; NMR refinement stuff =<br>; Distance restraints type: No, Simple or Ensemble =<br>disre =
No<br>; Force weighting of pairs in one distance restraint:<br>Equal or Conservative =<br>disre-weighting = Equal<br>; Use sqrt of the time averaged times the<br>instantaneous violation =<br>disre-mixed = no
<br>disre-fc = 1000<br>disre-tau = 0<br>; Output frequency for pair distances to energy file =<br>nstdisreout = 100<br><br>; Free energy control stuff =<br>free-energy = no
<br>init-lambda = 0<br>delta-lambda = 0<br><br>; Non-equilibrium MD stuff =<br>acc-grps =<br>accelerate =<br>freezegrps = Protein POPC SOL<br>freezedim = Y Y Y Y Y Y Y Y Y
<br>; Electric fields =<br>; Format is number of terms (int) and for all terms an<br>amplitude (real) =<br>; and a phase angle (real) =<br>E-x =<br>E-xt =<br>E-y =
<br>E-yt =<br>E-z =<br>E-zt =<br><br>; User defined thingies =<br>user1-grps =<br>user2-grps =<br>user3-grps =<br>userint1 = 0
<br>userint2 = 0<br>userint3 = 0<br>userint4 = 0<br>userreal1 = 0<br>userreal2 = 0<br>userreal3 = 0<br>userreal4 = 0
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<br>-- <br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciencesand Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>
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