[gmx-users] Fibril not restrained?

Kevin Boyd kevin.boyd at uconn.edu
Thu Jun 7 21:26:17 CEST 2018


To apply the restraints in the topology you need to use the define
field in the mdp file. For your case, the option would be "define =
-DPOSRES_A". Otherwise that #ifdef statement will evaluate to false
and the restraints won't be included. Also, are there end quotes
around posre_Protein_chain_A.itp?

You can quickly assess whether the position restraints are actually
being implemented in the log file. If restraints are turned on, there
should be a position restraint energy term reported where the other
energy terms (ie LJ-short range, potential energy, kinetic energy,
temperature) are printed at regular step intervals. If you don't see a
position restraint term, the system wasn't properly set up.



On Thu, Jun 7, 2018 at 2:28 PM, Angelina Malagodi
<angelinamalagodi at gmail.com> wrote:
> Hello:
> I’m using 2beg.pdb and a modified version of the 2lmn.pdb fibril for several systems. The fibrils are quickly collapsing after the first step of production, even after including the posre restraints are called. I added the restraints by including:
> ; Include Position restraint file
> #ifdef POSRES_A
> #include “posre_Protein_chain_A.itp
> #endif
> at the end of the respective chain’s topology. When I visualize the system the initial frame looks like the system is restrained, but the fibrils collapse into a more spherical shape after the next frame.
> Is there anything else I can do to restrain the fibril during production?
> Thank you,
> Angelina
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