normal Inserting position restraints

  • Sithara Perera
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2 years 1 month ago #7225 by Sithara Perera
Inserting position restraints was created by Sithara Perera

I' making a 512 DPPC bi-layer out of 128 bilayer available in . The force field used is martini.

But once the energy minimization is done, the bi-layer crashes and accumulates to globules.

So I made an position.itp file using the command

gmx genrestr -f dppc221.gro -n test.ndx -o lipid_posre.itp -fc 1000 1000 1000

And included in the topology file.

Topology file also include

include "martini_v2.0.itp"
#include "martini_v2.0_lipids.itp" from martini as well.

But then when the command

gmx grompp -f minim.mdp -c dppc221.gro -p -o em2.tpr

is given , following error occurs.

Fatal error:
[ file posre.itp, line 29 ]:
Atom index (25) in position_restraints out of bounds (1-24).
This probably means that you have inserted topology section "position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.

How can I fix this?

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2 years 1 month ago #7226 by bart
Replied by bart on topic Inserting position restraints

I am not sure, maybe someone else would know, but to make a 512 lipids bilayer from scratch would not take more than a few minutes. You can use 'insane', a program developed by our lab which you can find under downloads (its part of the complex bilayer tutorial), or you could even do random assembly and be done within an hour. Of course this doesn't answer you question, but it might still help you continue you research. For sure I would not walk down the path of using constraints anyway. I could advise on doing the lipids tutorials anyway if you intend to use martini for that purpose. We just released the GMX 5 version.


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