<div>Dear all,</div>
<div> </div>
<div>It is the first time that I use gromacs 4.04 to calculate PMF. I have some question needed to be clarified.</div>
<div> </div>
<div>1. </div>
<div>;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<br>; pull code for PMF<br>pull = Unbrella ;unbrella,constraint <br>pull_geometry = Distance ;distance ,direction,cylinder,position<br>
pull_dim = N N Y<br>pull_group0 = DPPC<br>pull_group1 = DEN<br>pull_nstxout = 100<br>pull_nstfout = 100<br>pull_init1 = 3.8</div>
<div>pull_k1 = 1000 </div>
<div> </div>
<div>Is there any relationship between the steps for pull_nstxout and pull_nsfout. Must they be the same( e.g. 100, 100)? How to choose them?</div>
<div> </div>
<div>2. It seems that there are only two output file: pullx.xvg and pullf.xvg. Is it right? are there other files for the input of g_wham?</div>
<div> </div>
<div>3. What other thing I must take care of for calculation of PMF</div>
<div> </div>
<div>Thanks in advance.<br clear="all"><br>-- <br>wende<br></div>