[gmx-users] constraint pulling

leila karami karami.leila1 at gmail.com
Wed Mar 19 10:07:10 CET 2014

Dear Justin

My system contains lipid + drug + water molecules.

At first, I put drug molecule in middle of bilayer.

Based on your tutorial, after minimization and equilibration, I generated
configurations. After using distance.pl script, summary_distances.dat file
is irregular such that no increasing trend is not seen in the distances. Some
times distance increased and some time decreased.

Is there problem in generating configuration step?

pull code part of mdp file is as follows:

pull = constraint
pull_geometry = distance
pull_constr_tol = 1e-6
pull_dim = N N Y
pull_ngroups    = 1
pull_group0     = CHOL_DOPC
pull_group1     = drug
pull_vec1 = 0 0 1
pull_rate1= 0
pull-start = yes

How to resolve this issue?

Best wishes

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