<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div id="yiv1482801195"><div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-family: times new roman,new york,times,serif; font-size: 12pt;"><div><br></div><div>Hi everybody,</div><div><br></div><div>I just ran a number of simulations with two large and roughly spherical molecules</div><div>in a primitive model electrolyte (epsilon=80), they are constrained to the z-axes and</div><div>i calculate the PMF using the pull code restraining the distance between the</div><div>two molecules. integration is done with langevin dynamcs (gmx-4.5.3)<br></div><br>what i see is this: I start several runs all with the same initial orientations of the two<br>molecules only the distance varies, the dynamics seems to go well, but when i compare<br><div>the FINAL ORIENTATIONS of the two molecules after multiple runs at
different</div><div>distances they are NEARLY THE SAME not matter which distance i choose.</div><div><br></div><div>below is the relevant part of my mdp file:<br></div><div><br>
</div>
<div>integrator = sd<br>
tau_t = 2.0<br>
ref_t = 300<br>
gen_vel = yes<br>
gen_temp = 240.0<br>
gen_seed = xxx ; this varies<br>
tc_grps = System<br>
nsteps = 200000<br>
dt = 0.001</div><div><br></div><div>The forces depend on the distance of course (the molecules have</div><div>a heterogeneous charge distribution) and this is a highly chaotic system</div><div>therefore the probability that the conformations (basically the</div><div>rotational DOFs of the two molecules) are the same or very similar after</div><div>200 ps at 300K should basically be ZERO ... but this is what i see, <br></div><div>its re-producible and happens at different distances AND with different</div><div>molecular topologies (charge distributions).<br></div><div><br></div><div>a possible explanation for this behaviour might be that of the terms <br></div><div>in eqn. 3.108 only the velocity dependent and the random term are actually<br>considered but not force term AND gen_seed doesn't make any difference for <br>SD ...
then the small differences i see would be only from round-off errors ... ???</div><div><br></div><div>has anybody seen something similar ?</div><div><br></div><div>i'd appreciate any suggestions!</div><div><br></div><div>thanks</div><div>Michael</div><div><br></div></div></div> </div></body></html>