<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US>Dear all:</SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><SPAN style="mso-tab-count: 1"> </SPAN>I’m using Gromacs-<?xml:namespace prefix = st1 ns = "urn:schemas-microsoft-com:office:smarttags" /><st1:chsdate w:st="on" Year="1899" Month="12" Day="30" IsLunarDate="False" IsROCDate="False"><st1:chsdate w:st="on" Year="1899" Month="12" Day="30" IsLunarDate="False" IsROCDate="False">4.0.5</st1:chsdate> a</st1:chsdate>nd 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. </SPAN></P>
<P style="TEXT-INDENT: 21pt; MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US>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)”.</SPAN></P>
<P style="TEXT-INDENT: 21pt; MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US>So here are my doubts about this simulation:</SPAN></P>
<P style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 18pt; mso-list: l0 level1 lfo1; tab-stops: list 18.0pt" class=MsoNormal><SPAN style="mso-fareast-font-family: 'Times New Roman'" lang=EN-US><SPAN style="mso-list: Ignore">1.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN></SPAN><SPAN lang=EN-US>Can Gromacs-<st1:chsdate w:st="on" Year="1899" Month="12" Day="30" IsLunarDate="False" IsROCDate="False">4.0.5</st1:chsdate> do this for me, especially keeping the C atoms immobile in X and Y direction while moving along the Z direction?</SPAN></P>
<P style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 18pt; mso-list: l0 level1 lfo1; tab-stops: list 18.0pt" class=MsoNormal><SPAN style="mso-fareast-font-family: 'Times New Roman'" lang=EN-US><SPAN style="mso-list: Ignore">2.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN></SPAN><SPAN lang=EN-US>In my simulation, every carbon atom in the slab of griphene was defined as a group. Is it right?</SPAN></P>
<P style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 18pt; mso-list: l0 level1 lfo1; tab-stops: list 18.0pt" class=MsoNormal><SPAN style="mso-fareast-font-family: 'Times New Roman'" lang=EN-US><SPAN style="mso-list: Ignore">3.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN></SPAN><SPAN lang=EN-US>How to give the “</SPAN><STRONG><SPAN style="COLOR: red; mso-bidi-font-size: 10.5pt" lang=EN-US>pull_weights<st1:chmetcnv w:st="on" UnitName="”" SourceValue="1" HasSpace="False" Negative="False" NumberType="1" TCSC="0">1<SPAN style="COLOR: windowtext; FONT-WEIGHT: normal; mso-bidi-font-size: 12.0pt">”</SPAN></st1:chmetcnv></SPAN></STRONG><SPAN lang=EN-US> to avoid the above ERROR? </SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt 18pt" class=MsoNormal><SPAN lang=EN-US>Any suggestions and answers are welcome. Thank you in advance!</SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt 18pt" class=MsoNormal><SPAN lang=EN-US></SPAN> </P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN style="mso-bidi-font-size: 10.5pt" lang=EN-US>; 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 r<st1:chmetcnv w:st="on" UnitName="in" SourceValue="0" HasSpace="True" Negative="False" NumberType="1" TCSC="0">0 in</st1:chmetcnv> 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><STRONG><SPAN style="COLOR: red">pull_ngroups = 700</SPAN></STRONG><BR>; <SPAN class=ttag>Group</SPAN> 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><STRONG><SPAN style="COLOR: red">pull_weights1 = 1</SPAN></STRONG><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</SPAN></P>