<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt">Hi all,<br> Just one thing to add. Generally for PMF calculation the pulling is done in one direction (N N Y in mdp file for pulling in z direction). But, as I will be pulling a protein, I think, it will be Y Y Y i.e. in all directions. Is that OK? If that so, would I be able to calculate PMF in the conventional way? <br>Please suggest.<br>Thanks<br>Samrat Pal <br><div><br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Samrat Pal <psamrat10@yahoo.com><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users
<gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Tue, July 27, 2010 2:59:01 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Jarzynski equality in pulling simulation<br></font><br>
<meta http-equiv="x-dns-prefetch-control" content="off"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div>Dear All,<br> I am trying to do unfolding simulation of a protein by applying pulling code in GROMACS. Now, as the pulling speed is much more faster than the optical trap experiment or the AFM experiment, what would be more logical to get the PMF/free energy of the simulation -<br><br>(1) running multiple trajectories and apply Jarzynski equality to get free energy <br> OR <br>(2) running a single trajectory and taking configurations at different distances and then apply umbrella sampling to compute PMF.<br><br>Please
advise. <br>Thanks in advance,<br>Samrat Pal<br></div>
</div><br>
<meta http-equiv="x-dns-prefetch-control" content="on"></div></div>
</div><br>
</body></html>