<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">Hi,</div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "> I am performing steered Molecular dynamics simulation to pull a molecule out of a complex. I am using gromacs 4.5.4 to perform the constant rate pulling..I have done the steered MD simulation in a particular direction i.e hav pulled the molecule out of complex.</div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">But, to check the convergence/hysterisis of the pulled path way, I would like to perform the same steered MD in reverse direction i.e push the molecule back into the complex. But, I was wondering, to perform the backward steered MD, how should I modify the .mdp parameters? Should
I make the pull_rate1 negative or switch the pull_group0 and pull_group1 ? Any help will be appreciated.</div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><br></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">The following is the part of the pull-code parameter I am using:</div><div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">; Pull code</font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">pull = umbrella</font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">pull_geometry = distance ; simple distance increase</font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">pull_dim = N N Y</font></div><div><font
class="Apple-style-span" face="'times new roman', 'new york', times, serif">pull_start = yes ; define initial COM distance > 0</font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">pull_ngroups = 1</font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">pull_group0 = Mol_A</font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">pull_group1 = Mol_B</font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">pull_rate1 = 0.0025 ; 0.01 nm per ps = 10 nm per ns</font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">pull_k1 = 1000 ; kJ mol^-1 nm^-2</font></div></div><div
style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "> </div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><br></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">Sanku</div></div></body></html>