<P>Dear all:</P>
<P>These days, I am trying to pull a slab of griphene moving along the Z direction at a constant speed. The slab of griphene contains 700 atoms. After several times of E-mail communication with the Gromacs users, the simulation can run. However, the run didn't produce the results which I expected. Part of my .gro file and .mdp file are below. By using them, the COM of the slab of griphene moved at a constant speed, but the 'slab' crashed. Because not all the carbon atoms moved at the same speed.</P>
<P>In order to produce the results that I want, which pull type (<SPAN style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 10.5pt; mso-fareast-font-family: ËÎÌå; mso-font-kerning: 1.0pt; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US>no, umbrella, constraint or constant_force</SPAN>) and which pull geometry (<SPAN style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 10.5pt; mso-fareast-font-family: ËÎÌå; mso-font-kerning: 1.0pt; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US>distance, direction, cylinder or position</SPAN>) shall I use? There is no reference group in my simulation. Do I need to modify the .gro file?</P>
<P> </P>
<P>Part of the .gro file:</P>
<P>...</P>
<P> 4876sla C11052 3.608 0.748 0.237 0.0000 -0.0000 0.0001<BR> 4877sla C11053 3.821 0.871 0.237 0.0000 -0.0000 0.0001<BR> 4878sla C11054 0.000 0.871 0.237 0.0000 -0.0000 0.0001<BR> 4879sla C11055 3.892 0.748 0.237 0.0000 -0.0000 0.0001<BR> 4880sla C11056 0.017 0.748 0.237 0.0000 -0.0000 0.0001<BR> 4881sla C11057 3.395 1.117 0.237 0.0000 -0.0000 0.0001<BR> 4882sla C11058 3.679 1.117 0.237 0.0000 -0.0000 0.0001<BR> 4883sla C11059 3.466 0.994 0.237 0.0000 -0.0000 0.0001<BR> 4884sla C11060 3.608 0.994 0.237 0.0000 -0.0000 0.0001<BR> 4885sla C11061 3.821 1.117 0.237 0.0000 -0.0000 0.0001<BR> 4886sla C11062 0.000 1.117 0.237 0.0000 -0.0000 0.0001<BR>...</P>
<P>These are all the carbon atoms of the slab of griphene.</P>
<P> </P>
<P>; COM PULLING <BR>; Pull type: no, umbrella, constraint or constant_force<BR>pull = constraint<BR>; Pull geometry: distance, direction, cylinder or position<BR>pull_geometry = direction<BR>; Select components for the pull vector. default: Y Y Y<BR>pull_dim = N N Y<BR>; Cylinder radius for dynamic reaction force groups (nm)<BR>pull_r1 = 1<BR>; Switch from r1 to r0 in case of dynamic reaction force<BR>pull_r0 = 1.5<BR>pull_constr_tol = 1e-06<BR>pull_start = no<BR>pull_nstxout = 10<BR>pull_nstfout = 10<BR>; Number of pull groups <BR>pull_ngroups = 1<BR>; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)<BR>pull_group0 = <BR>pull_weights0 = <BR>pull_pbcatom0 = 0<BR>pull_group1 = sla<BR>pull_weights1 = <BR>pull_pbcatom1 = 0<BR>pull_vec1 = 0.0 0.0 1.0<BR>pull_init1 = 0.237<BR>pull_rate1 = 5e-4<BR>pull_k1 = <BR>pull_kB1 = </P>
<P> </P>
<P>Any suggestions are welcome! Thank you in advance!</P>