Dear Gromacs users:<br><br>I am trying cylinder pulling as an option of umbrella sampling using gromacs 4.0.7. Things seem to work but I noticed that in the output file pullx.xvg, the referece group's postion is always 0. I don't think it is right. When I use position pulling, the reference position is never 0. <br>
<br>Thanks for you help.<br>Kun<br><br>Below is my .mdp file <br>pull = umbrella<br>pull_geometry = cylinder<br>pull_r1 = 1.0<br>Pull_r0 = 1.0<br>pull_dim = N N Y<br>
pull_start = yes<br>pull_init1 = 0.0<br>pull_ngroups = 1<br>pull_group0 = group0<br>pull_group1 = group1<br>pull_rate1 = 0.01 <br>pull_vec1 = 0.0 0.0 -1.0<br>
pull_k1 = 3000 ; kJ mol^-1 nm^-2<br>pull_nstxout = 1000<br>pull_nstfout = 1000<br><br>Here is the output:<br><br>@ title "Pull COM"<br>@ xaxis label "Time (ps)"<br>
@ yaxis label "Position (nm)"<br>@TYPE xy<br>@ view 0.15, 0.15, 0.75, 0.85<br>@ legend on<br>@ legend box on<br>@ legend loctype view<br>@ legend 0.78, 0.8<br>@ legend length 2<br>@ s0 legend "0 Z"<br>
@ s1 legend "1 dZ"<br>0.0000 0 5.69818<br>2.0000 0 5.67685<br>4.0000 0 5.68564<br>6.0000 0 5.65461<br>8.0000 0 5.63482<br>10.0000 0 5.61658<br>12.0000 0 5.61679<br>14.0000 0 5.54434<br>16.0000 0 5.55352<br>
18.0000 0 5.4964<br><br><br>