<div> Dear Gromacs users,</div> <div> To what extent is the distance between two molecules constrained?</div> <div> My question is because I have run a g_dist to check the distance</div> <div> and it was not what I expected. Then I did a test and ran a g_dist before</div> <div> and after the mdrun and I found that the distance changes. Why is this??</div> <div>Where am I doing something wrong??</div> <div> </div> <div> I include my md.mdp file and my constraint.ppa file.</div> <div> </div> <div>md.mdp</div> <div>-----------------------</div> <div>define = -DFLEXIBLE<BR>integrator = md<BR>dt =
0.004<BR>nsteps = 5000; 20 ps!<BR>constraints = all-bonds<BR>nstxout = 100<BR>nstvout = 100<BR>nstlog = 100<BR>nstenergy = 100<BR>nstxtcout = 200<BR>energygrps = Complex_A
Complex_B<BR>rlist = 1<BR>rcoulomb = 1<BR>rvdw = 1</div> <div>tcoupl = Berendsen<BR>tc-grps = Complex_A Complex_B SOL_NA+<BR>tau_t = 0.004 0.004 0.004<BR>ref_t =
300 300 300</div> <div>gen_vel = no<BR>gen_temp = 300<BR>gen_seed = 173529</div> <div> </div> <div> </div> <div> </div> <div>constraint.ppa</div> <div>--------------------------------<BR>verbose = yes<BR>runtype = constraint<BR>group_1 = Complex_A<BR>reference_group = Complex_B<BR>reftype = com_t0<BR>reflag = 1<BR>constraint_direction = 1.0 1.0 1.0<BR>constraint_tolerance = 0.010<BR></div> <div> </div> <div> Can U plz help me to solve this problem! I also have one question to the</div> <div> constraint-direction, if I set this to "0 0 0" then what do I
constraint??</div> <div> </div> <div> Thanks,</div> <div> Soren</div>