normal Martini Elendyn -p backbone question

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1 month 3 weeks ago - 1 month 3 weeks ago #8177 by daniloboskovic
Martini Elendyn -p backbone question was created by daniloboskovic
So i did "-p backbone" in my "martinize.py" command and equilibriated with restraints (hopefully) using "-r .tpr" file from my energy minimization output. Did it include the position restraints ? I only had the tpr file, the gro file and an itp file which was included in the top file so when i ran my commands i presume the restraints are inside the gro/tdp file already? The tutorial says that only the MDP file should be edited to include restraints from an external file but does not state whether i should use -r .tpr from energy minimisation or something else.

Output:

Reading file 01-em.tpr, VERSION 2018.7 (single precision)
Reading file 01-em.tpr, VERSION 2018.7 (single precision)
The center of mass of the position restraint coord's is 7.865 7.922 3.708
Reading file 01-em.tpr, VERSION 2018.7 (single precision)
Reading file 01-em.tpr, VERSION 2018.7 (single precision)
The center of mass of the position restraint coord's is 7.865 7.922 3.708
Analysing residue names:
There are: 131 Protein residues
There are: 7227 Other residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group System is 22428.00
Last edit: 1 month 3 weeks ago by daniloboskovic. Reason: wrote tdp instead of tpr

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3 weeks 6 days ago #8209 by bart
Replied by bart on topic Martini Elendyn -p backbone question
The constraints are in the itp file. Either you have a separate constraint itp or they are inside the protein itp toggled by a wrapping if statement. The condition of the if statement in the itp is triggered by the value of a global variable which you can set in many ways, but most usually you specify it in the mdp file. I use the following line in the top of the mdp.

define = -DPOSRES

The actual if statement checks the POSRES, however if you specify a variable like this in an mdp you should prepend it with -D.

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