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On 13/04/2012 3:08 AM, Qinghua Liao wrote:
<blockquote
cite="mid:CA+y1NruBPQ93URno5vLO4tzwTQwS2=BrWbWp4cyCHn04LNcHfw@mail.gmail.com"
type="cite">Dear gmx users,
<div><br>
</div>
<div><font size="4">I tried to apply distance restraints to my
system, but I found that it failed because the distance
between the restraints atoms in the last frame is bigger than
what we want.</font></div>
</blockquote>
<br>
Distance restraints aren't magic. There has to be an accessible
simulation path from your initial conditions to one that satisfies
the restraints. So far you haven't found one - there need not be
one.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CA+y1NruBPQ93URno5vLO4tzwTQwS2=BrWbWp4cyCHn04LNcHfw@mail.gmail.com"
type="cite">
<div><font size="4"> </font><span style="font-size:large">Here are
the parameters for distance restraints in the topology file:</span></div>
<div><br>
</div>
<div>
<div>[ distance_restraints ]</div>
<div>; ai aj type index type’ low up1 up2 fac</div>
<div> 8 192 1 0 1 0.0 0.3 0.4 2.5</div>
<div> 18 203 1 0 1 0.0 0.3 0.4 2.5</div>
<div> 20 205 1 0 1 0.0 0.3 0.4 2.5</div>
</div>
<div><br>
</div>
<div><font size="4">and also I tried this (added four other
distance restraints in the same two groups):</font></div>
<div>
<div>[ distance_restraints ]</div>
<div>; ai aj type index type’ low up1 up2 fac</div>
<div> 7 193 1 0 1 0.0 0.3 0.4 2.5</div>
<div> 8 192 1 0 1 0.0 0.3 0.4 2.5</div>
<div> 11 195 1 0 1 0.0 0.3 0.4 2.5</div>
<div> 18 202 1 0 1 0.0 0.3 0.4 2.5</div>
<div> 20 202 1 0 1 0.0 0.3 0.4 2.5</div>
<div> 18 203 1 0 1 0.0 0.3 0.4 2.5</div>
<div> 20 205 1 0 1 0.0 0.3 0.4 2.5</div>
</div>
<div><br>
</div>
<div><font size="4">I am sure that the atom numbers are right.</font></div>
<div><font size="4">And the following lines are the mdp file I
used:</font></div>
<div><br>
</div>
<div>
<div>title = PDXN of Abeta in H2O</div>
<div>;cpp = /lib/cpp ; prepocessor of the
current machine</div>
<div>define = ;-DPOSRES </div>
<div>integrator = md ; molecular dynamics
algorithm</div>
<div>tinit = 0.0 ; start time and timestep
in ps</div>
<div>dt = 0.002 ; time step in ps</div>
<div>nsteps = 1000000 ; number of steps for 1000
ns run</div>
<div>emtol = 100 ; convergence criterion</div>
<div>emstep = 0.05 ; intial step size</div>
<div>nstlist = 0 ; step frequency for
updating neighbour list</div>
<div>ns_type = simple ;grid ; method for
neighbour searching (?)</div>
<div>nstxout = 5000 ; frequency for writing
coords to output .trr file</div>
<div>nstvout = 0 ; frequency for writing
velocities to output...should be same as nstxout</div>
<div>nstfout = 0 ; frequency for writing
forces to output</div>
<div>nstlog = 5000 ; frequency for writing
energies to log file</div>
<div>nstenergy = 5000 ; frequency for writing
energies to energy file</div>
<div>nstxtcout = 5000 ; frequency for writing
coords to xtc traj</div>
<div>xtc_grps = system ; group(s) whose coords are
to be written in xtc traj</div>
<div>energygrps = system ; group(s) whose energy is
to be written in energy file</div>
<div><br>
</div>
<div><span style="background-color:rgb(255,255,0)">;distance
restraints</span></div>
<div><span style="background-color:rgb(255,255,0)">disre
= simple</span></div>
<div><span style="background-color:rgb(255,255,0)">disre_fc
= 20000 <font size="4">; for the force, I tried
3000, 6000, 10000 and 15000, but all the tests failed</font></span></div>
<div><span style="background-color:rgb(255,255,0)">disre_mixed
= yes</span></div>
<div><span style="background-color:rgb(255,255,0)">disre_weighting
= equal</span></div>
<div><span style="background-color:rgb(255,255,0)">disre_tau
= 10</span></div>
<div><span style="background-color:rgb(255,255,0)">nstdisreout
= 100</span></div>
<div>;</div>
<div>comm_mode = angular</div>
<div>nstcomm = 10</div>
<div>comm_grps = system</div>
<div>;</div>
<div>pbc = no ;xyz ; use pbc</div>
<div>rlist = 0 ;1.4 ; cutoff lengths (nm)</div>
<div>epsilon_r = 1.0 ; Dielectric constant (DC)
for twin-range or DC of reaction field</div>
<div>niter = 100 ; Some thingies for future
use </div>
<div>fourierspacing<span class="Apple-tab-span"
style="white-space:pre"> </span> = 0.16</div>
<div>fourier_nx = 30</div>
<div>fourier_ny = 30</div>
<div>fourier_nz = 30</div>
<div>coulombtype = Cut-off ; truncation for
minimisation, with large cutoff</div>
<div>rcoulomb = 0 ;1.4</div>
<div>rcoulomb-switch = 0</div>
</div>
<div>
<div>vdw-type = Cut-off ; truncation for
minimisation, with large cutoff</div>
<div>rvdw-switch = 0</div>
<div>rvdw = 0 ; 1.4 ; cut-off lengths</div>
<div>;pme_order = 6 ; EWALD/PME/PPPM
parameters</div>
<div>;ewald_rtol = 1e-05</div>
<div>;ewald_geometry = 3d</div>
<div>epsilon_surface = 0</div>
<div>optimize_fft = yes</div>
<div> Free energy control stuff</div>
<div>free_energy = yes</div>
<div>init_lambda = 0.0</div>
<div>delta_lambda = 0</div>
<div>sc_alpha =0.5</div>
<div>sc-power =1.0</div>
<div>sc-sigma = 0.3</div>
<div>;nstcomm = 0 ; number of steps for
centre of mass motion removal (in vacuo only!)</div>
<div>Tcoupl = V-rescale ;Berendsen</div>
<div>tc_grps = system ;Other Water_and_ions</div>
<div>tau_t = 0.5 ; 0.5 </div>
<div>ref_t = 300 ; 300</div>
<div>Pcoupl = no</div>
<div>;Pcoupltype = Isotropic</div>
<div>;tau_p = 1.0 1.0 1.0</div>
<div>
;ref_p = 1.0 1.0 1.0</div>
<div>;compressibility = 4.5e-5 ; compressibility</div>
<div>annealing = no ; SIMULATED ANNEALING
CONTROL </div>
<div>;zero_temp_time = 0 ; Time at which
temperature should be zero (ps)</div>
<div>gen_vel = yes</div>
<div>gen_temp = 300</div>
<div>gen_seed = -1</div>
<div>constraints = all-bonds ; OPTIONS FOR BOND
CONSTRAINTS </div>
<div>constraint-algorithm = Lincs ; Type of constraint
algorithm</div>
<div>lincs_order = 4 ; Highest order in the
expansion of the constraint coupling matrix</div>
<div>lincs_warnangle = 30 ; Lincs will write a
warning to the stderr if in one step a bond rotates </div>
<div> ; over more degrees than </div>
<div>unconstrained-start = no ; Do not constrain the
start configuration</div>
<div>;Shake-SOR = no ; Use successive
overrelaxation to reduce the number of shake iterations</div>
<div>;shake-tol = 1e-04 ; Relative tolerance of
shake</div>
<div>morse = no ; Convert harmonic bonds to
morse potentials</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div><font size="4">Could someone help me to figure it out? Is
there some parameter that I missed to add? Thanks very much~</font></div>
<div>
<div><br>
</div>
-- <br>
Best Regards,
<div><br>
</div>
<div>Qinghua</div>
<div><br>
</div>
<br>
</div>
<br>
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</blockquote>
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