[gmx-users] Fibril not restrained?
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
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:
> 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
> 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,
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