<div dir="ltr">Hello,<br><br>I am doing umbrella sampling to calculate PMF curve for the detachment of a terminal cyclic peptide with 8 aa's (CP) from the self-assembled cyclic peptide nanotube. I extracted the reaction coordinates staring from 5.5 ang COM distance between the terminal CP and the 2nd CP to 17.5 ang, I did umbrella sampling on 25 configurations (for 5ns) and the window size is 0.5 ang. I used the following pulling code for umbrella sampling,<br>
<br>pull = umbrella<br>pull_geometry = distance<br>pull_dim = N N Y<br>pull_start = yes <br>pull_ngroups = 1<br>pull_group0 = Chain_B <br>pull_group1 = Chain_A <br>pull_init1 = 0<br>
pull_rate1 = 0.0<br>pull_k1 = 1000 <br>pull_nstxout = 1000 <br>pull_nstfout = 1000 <br><br><br>I restrained the 2nd CP unit and the pull_rate1 is 0, so the COM distance between the chain_A (terminal) and chain_B (2nd CP) should be restrained. after 5ns of umbrella sampling, I calculated the COM distance between chain A and B, but it was not restrained, for the 5.5 ang COM distance restrain, the COM distance varies from 4.5 to 5.5 ang. and also the pulling cyclic peptide undergoes large conformational sampling. from the WHAM analysis I understood the sampling window is poorly represented. In addition to COM distance restrain, can I restrain the pulling CP's backbone atoms? so that the pulling groups large conformational sampling will be reduced. <br>
I am using gromacs 4.5.5 version. <br>Regards,<br>Vijay.<br></div>