[gmx-users] wanted to fix cpn in lipid layer MD, -position/distance restrains

Christopher Neale chris.neale at alum.utoronto.ca
Tue Apr 12 19:44:22 CEST 2016

This is not enough detail for us to know what the problem is. Did you set things up correctly so that posre_cpn.itp is actually used? You can check by gmx energy and see if you have restraint energies there. To use these restraints your .top file needs to #include "posre_cpn.itp" , which you can do directly or via an #ifdef statement in the cpn.itp topology and define=-DSOME_IDENTIFIER in your .mdp file .... you can see how this is done in your .top file for water.


From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Nikhil Maroli <scinikhil at gmail.com>
Sent: 12 April 2016 09:25
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] wanted to fix cpn in lipid layer MD,       -position/distance restrains

Dear all,
i am doing MD of cyclic peptide nanotube in lipids,i wanted to keep the
tube fixed thoughout simulation but with below restrains after 40ns two to
three rings moves away from the positions .

gmx genrestr -f cpn.gro -o posre_cpn.itp -fc 1000 1000 1000

i wanted to  keep the position  fixed or maximum +1 nm movements of
individual rings , so can anyone suggest

me how should i proceed  i dont have time to check all the possibility
of gmx genrestr

so specifically hwo should i procees in such cases


Nikhil Maroli
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