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On 30/05/2012 5:33 PM, MD wrote:
<blockquote
cite="mid:1dc9ba2d.c95b.1379caa467e.Coremail.ptf1242@163.com"
type="cite">
<div style="line-height: 1.7; color: rgb(0, 0, 0); font-size:
14px; font-family: arial;">
<div>Hi All,</div>
<div> </div>
<div>I have to use the long range correction for VDW, in fact i
used cut-off=1.4 nm for calculation of surface tension of
TIP4P/2005, we can get 65 dyn. The .mdp i used are as follow,
I really need to know how to get a surface tension of 69.5 dyn
for TIP4P/2005 water model.</div>
</div>
</blockquote>
<br>
By finding the method that was used then and attempting to replicate
it?<br>
<br>
<blockquote
cite="mid:1dc9ba2d.c95b.1379caa467e.Coremail.ptf1242@163.com"
type="cite">
<div style="line-height: 1.7; color: rgb(0, 0, 0); font-size:
14px; font-family: arial;">
<div> Becasue my surpervisor is so picky, everything should be
perfacet, and i feel really tired by his way. Any comment will
be greatly appreciated,</div>
</div>
</blockquote>
<br>
A certain degree of pickiness is essential. You're apparently trying
to replicate a result by making some arbitrary choices. Don't.<br>
<br>
This .mdp file generates velocities, thus did not start in an
equilibrium ensemble. However you measured your surface tension
needs to exclude the equilibration time.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:1dc9ba2d.c95b.1379caa467e.Coremail.ptf1242@163.com"
type="cite">
<div
style="line-height:1.7;color:#000000;font-size:14px;font-family:arial">
<div> </div>
<div>The main parameter is </div>
<div> </div>
<div>
<p>coulombtype = PME</p>
<p>rcoulomb-switch = 0</p>
<p>rcoulomb = 1.4</p>
<p>; Dielectric constant (DC) for cut-off or DC of reaction
field</p>
<p>epsilon-r = 1</p>
<p>; Method for doing Van der Waals</p>
<p>vdw-type = Cut-off</p>
<p>; cut-off lengths </p>
<p>rvdw-switch = 0</p>
<p>rvdw = 3.8</p>
<p>; Apply long range dispersion corrections for Energy and
Pressure</p>
<p>DispCorr = EnerPres</p>
<p>; Extension of the potential lookup tables beyond the
cut-off</p>
<p>table-extension = 1</p>
<p>; Spacing for the PME/PPPM FFT grid</p>
<p>fourierspacing = 0.12</p>
<p> </p>
<p> </p>
<p> </p>
<p> </p>
<p>The full .mdp are as follow,</p>
<p> </p>
<p> </p>
</div>
<div><span lang="EN-AU">
<p>;</p>
<p>; File 'mdout.mdp' was generated</p>
<p>; By user: spoel (291)</p>
<p>; On host: chagall</p>
<p>; At date: Mon Dec 15 13:13:06 2003</p>
<p>;</p>
<p>; VARIOUS PREPROCESSING OPTIONS</p>
<p>title = Yo</p>
<p>cpp = /usr/bin/cpp</p>
<p>include = </p>
<p>define = </p>
<p>; RUN CONTROL PARAMETERS</p>
<p>integrator = md</p>
<p>; Start time and timestep in ps</p>
<p>tinit = 0</p>
<p>dt = 0.001</p>
<p>nsteps = 400000</p>
<p>; For exact run continuation or redoing part of a run</p>
<p>init_step = 0</p>
<p>; mode for center of mass motion removal</p>
<p>comm-mode = Linear</p>
<p>; number of steps for center of mass motion removal</p>
<p>nstcomm = 1</p>
<p>; group(s) for center of mass motion removal</p>
<p>comm-grps = </p>
<p>; LANGEVIN DYNAMICS OPTIONS</p>
<p>; Temperature, friction coefficient (amu/ps) and random
seed</p>
<p>bd-fric = 0</p>
<p>ld-seed = 1993</p>
<p>; ENERGY MINIMIZATION OPTIONS</p>
<p>; Force tolerance and initial step-size</p>
<p>; Max number of iterations in relax_shells</p>
<p>niter = 20</p>
<p>　</p>
<p>; OUTPUT CONTROL OPTIONS</p>
<p>; Output frequency for coords (x), velocities (v) and
forces (f)</p>
<p>nstxout = 5000</p>
<p>nstvout = 8000</p>
<p>nstfout = 8000</p>
<p>; Checkpointing helps you continue after crashes</p>
<p>nstcheckpoint = 1000</p>
<p>; Output frequency for energies to log file and energy
file</p>
<p>nstlog = 5000</p>
<p>nstenergy = 5000</p>
<p>; Output frequency and precision for xtc file</p>
<p>nstxtcout = 500</p>
<p>xtc-precision = 1000</p>
<p>; This selects the subset of atoms for the xtc file. You
can</p>
<p>; select multiple groups. By default all atoms will be
written.</p>
<p>xtc-grps = </p>
<p>; Selection of energy groups</p>
<p>energygrps = </p>
<p>; NEIGHBORSEARCHING PARAMETERS</p>
<p>; nblist update frequency</p>
<p>nstlist = 5</p>
<p>; ns algorithm (simple or grid)</p>
<p>ns_type = grid</p>
<p>; Periodic boundary conditions: xyz (default), no
(vacuum)</p>
<p>; or full (infinite systems only)</p>
<p>pbc = xyz</p>
<p>; nblist cut-off </p>
<p>rlist = 1.4</p>
<p>domain-decomposition = no</p>
<p>; OPTIONS FOR ELECTROSTATICS AND VDW</p>
<p>; Method for doing electrostatics</p>
<p>coulombtype = PME</p>
<p>rcoulomb-switch = 0</p>
<p>rcoulomb = 1.4</p>
<p>; Dielectric constant (DC) for cut-off or DC of reaction
field</p>
<p>epsilon-r = 1</p>
<p>; Method for doing Van der Waals</p>
<p>vdw-type = Cut-off</p>
<p>; cut-off lengths </p>
<p>rvdw-switch = 0</p>
<p>rvdw = 3.8</p>
<p>; Apply long range dispersion corrections for Energy and
Pressure</p>
<p>DispCorr = EnerPres</p>
<p>; Extension of the potential lookup tables beyond the
cut-off</p>
<p>table-extension = 1</p>
<p>; Spacing for the PME/PPPM FFT grid</p>
<p>fourierspacing = 0.12</p>
<p>; FFT grid size, when a value is 0 fourierspacing will be
used</p>
<p>fourier_nx = 0</p>
<p>fourier_ny = 0</p>
<p>fourier_nz = 0</p>
<p>; EWALD/PME/PPPM parameters</p>
<p>pme_order = 4</p>
<p>ewald_rtol = 1e-05</p>
<p>ewald_geometry = 3d</p>
<p>epsilon_surface = 0</p>
<p>optimize_fft = no</p>
<p>; GENERALIZED BORN ELECTROSTATICS</p>
<p>; Algorithm for calculating Born radii</p>
<p>gb_algorithm = Still</p>
<p>; Frequency of calculating the Born radii inside rlist</p>
<p>nstgbradii = 1</p>
<p>; Cutoff for Born radii calculation; the contribution
from atoms</p>
<p>; between rlist and rgbradii is updated every nstlist
steps</p>
<p>rgbradii = 2</p>
<p>; Salt concentration in M for Generalized Born models</p>
<p>gb_saltconc = 0</p>
<p>; IMPLICIT SOLVENT (for use with Generalized Born
electrostatics)</p>
<p>implicit_solvent = No</p>
<p>; OPTIONS FOR WEAK COUPLING ALGORITHMS</p>
<p>; Temperature coupling </p>
<p>Tcoupl = v-rescale</p>
<p>; Groups to couple separately</p>
<p>tc-grps = System</p>
<p>; Time constant (ps) and reference temperature (K)</p>
<p>tau_t = 0.1</p>
<p>ref_t = 300</p>
<p>; Pressure coupling </p>
<p>Pcoupl = no</p>
<p>Pcoupltype = isotropic</p>
<p>; Time constant (ps), compressibility (1/bar) and
reference P (bar)</p>
<p>tau_p = 1</p>
<p>compressibility = 4.5e-5</p>
<p>ref_p = 1.0</p>
<p>; Random seed for Andersen thermostat</p>
<p>andersen_seed = 815131</p>
<p>; SIMULATED ANNEALING </p>
<p>; Type of annealing for each temperature group
(no/single/periodic)</p>
<p>annealing = no</p>
<p>; Number of time points to use for specifying annealing
in each group</p>
<p>annealing_npoints = </p>
<p>; List of times at the annealing points for each group</p>
<p>annealing_time = </p>
<p>; Temp. at each annealing point, for each group.</p>
<p>annealing_temp = </p>
<p>; GENERATE VELOCITIES FOR STARTUP RUN</p>
<p>gen_vel = yes</p>
<p>gen_temp = 300</p>
<p>gen_seed = 1993</p>
<p>; OPTIONS FOR BONDS </p>
<p>constraints = none</p>
<p>; Type of constraint algorithm</p>
<p>constraint-algorithm = Lincs</p>
<p>; Do not constrain the start configuration</p>
<p>unconstrained-start = no</p>
<p>; Use successive overrelaxation to reduce the number of
shake iterations</p>
<p>Shake-SOR = no</p>
<p>; Relative tolerance of shake</p>
<p>shake-tol = 1e-04</p>
<p>; Highest order in the expansion of the constraint
coupling matrix</p>
<p>lincs-order = 4</p>
<p>; Number of iterations in the final step of LINCS. 1 is
fine for</p>
<p>; normal simulations, but use 2 to conserve energy in NVE
runs.</p>
<p>; For energy minimization with constraints it should be 4
to 8.</p>
<p>lincs-iter = 1</p>
<p>; Lincs will write a warning to the stderr if in one step
a bond</p>
<p>; rotates over more degrees than</p>
<p>lincs-warnangle = 30</p>
<p>; Convert harmonic bonds to morse potentials</p>
<p>morse = no</p>
<p>; ENERGY GROUP EXCLUSIONS</p>
<p>; Pairs of energy groups for which all non-bonded
interactions are excluded</p>
<p>energygrp_excl = </p>
<p>; NMR refinement stuff </p>
<p>; Distance restraints type: No, Simple or Ensemble</p>
<p>disre = No</p>
<p>; Force weighting of pairs in one distance restraint:
Conservative or Equal</p>
<p>disre-weighting = Conservative</p>
<p>; Use sqrt of the time averaged times the instantaneous
violation</p>
<p>disre-mixed = no</p>
<p>disre-fc = 1000</p>
<p>disre-tau = 0</p>
<p>; Output frequency for pair distances to energy file</p>
<p>nstdisreout = 100</p>
<p>; Orientation restraints: No or Yes</p>
<p>orire = no</p>
<p>; Orientation restraints force constant and tau for time
averaging</p>
<p>orire-fc = 0</p>
<p>orire-tau = 0</p>
<p>orire-fitgrp = </p>
<p>; Output frequency for trace(SD) to energy file</p>
<p>nstorireout = 100</p>
<p>; Dihedral angle restraints: No, Simple or Ensemble</p>
<p>dihre = No</p>
<p>dihre-fc = 1000</p>
<p>dihre-tau = 0</p>
<p>; Output frequency for dihedral values to energy file</p>
<p>nstdihreout = 100</p>
<p>; Free energy control stuff</p>
<p>free-energy = no</p>
<p>init-lambda = 0</p>
<p>delta-lambda = 0</p>
<p>sc-alpha = 0</p>
<p>sc-sigma = 0.3</p>
<p>; Non-equilibrium MD stuff</p>
<p>acc-grps = </p>
<p>accelerate = </p>
<p>freezegrps = </p>
<p>freezedim = </p>
<p>cos-acceleration = 0</p>
<p>; Electric fields </p>
<p>; Format is number of terms (int) and for all terms an
amplitude (real)</p>
<p>; and a phase angle (real)</p>
<p>E-x = </p>
<p>E-xt = </p>
<p>E-y = </p>
<p>E-yt = </p>
<p>E-z = </p>
<p>E-zt = </p>
<p>; User defined thingies</p>
<p>user1-grps = </p>
<p>user2-grps = </p>
<p>userint1 = 0</p>
<p>userint2 = 0</p>
<p>userint3 = 0</p>
<p>userint4 = 0</p>
<p>userreal1 = 0</p>
<p>userreal2 = 0</p>
<p>userreal3 = 0</p>
<p>userreal4 = 0</p>
</span></div>
<div id="divNeteaseMailCard"> </div>
<div> </div>
<div>The </div>
</div>
<br>
<br>
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<br>
</blockquote>
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