<P>Hi Carsten:</P>
<P>Thank you for your answers. I don't know whether I am right to reply to <A href="mailto:gmx-users@gromacs.org" target=_blank>gmx-users@gromacs.org</A>. If I am wrong, please tell me.</P>
<P>As in my last letter, I said I was not able to set "<SPAN style="FONT-FAMILY: 'Times New Roman'; COLOR: red; FONT-SIZE: 10.5pt; mso-fareast-font-family: 宋体; mso-font-kerning: 1.0pt; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US><STRONG>pull_weights1</STRONG></SPAN>" correctly. I have red the mannual, but I don't understand what it tells. I'll do with your recommendation, setting one pull group which contains 700 atoms and using Gromacs-4.0.7. Then how to set the "<SPAN style="FONT-FAMILY: 'Times New Roman'; COLOR: red; FONT-SIZE: 10.5pt; mso-fareast-font-family: 宋体; mso-font-kerning: 1.0pt; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US><STRONG>pull_weights1</STRONG></SPAN>" ?</P>
<P>Best regards!</P>
<P> </P>
<P> </P>
<P>Hi,<BR><BR>you should set one pull group, not 700. The number of atoms in your<BR>pull group is 700. Freezing the pull group in x and y direction probably<BR>does what you want. Please also consider to upgrade to 4.0.7,<BR>which is the most recent stable version.<BR><BR>Best,<BR> Carsten<BR><BR><BR>On Jan 22, 2010, at 7:41 AM, toby10222224@sina.com wrote:<BR><BR>> Dear all:<BR>> Im using Gromacs-4.0.5 and I want to use the pull code to pull a slab of griphene to move along the Z direction in the simulation (Steered Molecular Dynamics-SMD). The griphene has 700 carbon atoms and the positions of the 700 atoms are expected to be immobile in the X and Y direction.<BR>> The following is the PULL CODE in my mdp file. However, when I used this code for my simulation the error always came out as Number of weights (1) for pull group 1 'sla' does not match the number of atoms (700).<BR>> So here are my doubts about this simulation:<BR>> 1. Can Gromacs-4.0.5 do this for me, especially keeping the C atoms immobile in X and Y direction while moving along the Z direction?<BR>> 2. In my simulation, every carbon atom in the slab of griphene was defined as a group. Is it right?<BR>> 3. How to give the pull_weights1 to avoid the above ERROR?<BR>> Any suggestions and answers are welcome. Thank you in advance!<BR>> <BR>> ; COM PULLING <BR>> ; Pull type: no, umbrella, constraint or constant_force<BR>> pull = constant_force<BR>> ; Pull geometry: distance, direction, cylinder or position<BR>> pull_geometry = distance<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 = <BR>> ; Switch from r1 to r0 in case of dynamic reaction force<BR>> pull_r0 = <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 = 700<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 = <BR>> pull_group1 = sla<BR>> pull_weights1 = 1<BR>> pull_pbcatom1 = 0<BR>> pull_vec1 = 0.0 0.0 1.0<BR>> pull_init1 = 0.0<BR>> pull_rate1 = 0<BR>> pull_k1 = 1.2e-4<BR>> pull_kB1 = 0<BR></P>