<div dir="ltr"><div>Hi,</div>
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<div>my system is constructed of 2 parallel plates in a box with solvent. each plate is made of 36 atoms which are positively charged on one of them (SRP) and negatively charged on the other plate (SRN).</div>
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<div>i want to perform a simulation with umbrella sampling between the 2 so i defined the pulling section parameters in the .mdp parameter file as following:</div>
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<div>; COM PULLING <br>; Pull type: no, umbrella, constraint or constant_force<br>pull = umbrella<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 = Y Y 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 = 1<br>; Number of pull groups <br>pull_ngroups = 2<br>
; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)<br>pull_group0 = SRP<br>pull_weights0 = 1<br>pull_pbcatom0 = 0<br>pull_group1 = SRN<br>pull_weights1 = 1<br>
pull_pbcatom1 = 0<br>pull_vec1 = 0.0 1.0 0.0<br>pull_init1 = 1.5<br>pull_rate1 = 0<br>pull_k1 = 1<br>pull_kB1 = 0</div>
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<div>when proccesing the file with grompp i get the following error:</div>
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<div><strong>Fatal error:<br>Number of weights (1) for pull group 0 'SRP' does not match the number of atoms (36)</strong></div>
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<div>is someone recognizing my mistake? </div>
<div>does someone has an experience with umbrella sampling in GROMACS?</div>
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<div>thanks'</div>
<div>amir</div>
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