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><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>
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