<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span><div>Thanks for the suggestion.</div><div><span> Also, I was wondering how one can get the time profile of the irreversible work from the gromacs pull-code out put . From constant pulling-rate SMD, we get time profile of force pullf.xvg and pullx.xvg. I wonder does multiplying the the value from pullx.xvg and value from pullf.xvg will provide the work . Or, will it be force ( obtained from pullf.xvg) multiplied by pulling rate multiplied by time ?</span></div></span></div><div><br></div><div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "><div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "><font size="2" face="Arial"><hr size="1"><b><span style="font-weight:bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br><b><span
style="font-weight: bold;">To:</span></b> Sanku M <msanku65@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Thursday, November 3, 2011 9:27 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Steered MD in reverse direction?<br></font><br>
<br><br>Sanku M wrote:<br>> Hi,<br>> 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.<br>> 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.<br>> <br><br>Use a negative pull rate. But simple pulling like this can be difficult; you're now trying to hit a moving target. A slight rotation of the protein can render the whole simulation junk - your pulled molecule may smack into
some undesired location.<br><br>-Justin<br><br>> The following is the part of the pull-code parameter I am using:<br>> ; Pull code<br>> pull = umbrella<br>> pull_geometry = distance ; simple distance increase<br>> pull_dim = N N Y<br>> pull_start = yes ; define initial COM distance > 0<br>> pull_ngroups = 1<br>> pull_group0 = Mol_A<br>> pull_group1 = Mol_B<br>> pull_rate1 = 0.0025 ; 0.01 nm per ps = 10 nm per ns<br>> pull_k1 = 1000 ; kJ mol^-1 nm^-2<br>> <br>> Sanku<br>> <br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia
Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br><br>========================================<br><br><br></div></div></div></body></html>