Dear all,
I am
I am looking to replicate the figure attached with this post. The paper attached tells that the authors established a temperature gradient between a protein ( which cooled to 300 K from 400 K) where as the water bath i.e. the solvent temperature remained constant at 300 K.
I have prepared my system such that water is at 300 K and protein is at 400 K by using standard equilibration protocols and simulated annealing in GROMACS. The authors of the paper describe that they removed the thermostat from the protein and let it relax keeping the solvent (water) at 300 K.
But if I remove thermostat , I get GROMACS error and using freeze groups I am not getting any temperatures as the molecules are not moving.
I can not understand how to model this system. Any suggestions will be helpful. I am doing a literature search but till now it is not fruitful.
Best,
How about to give the protein a very large temperature coupling time, e.g. >1ns?
The problem was fixed by using a negative coupling constant. I was helped out at the GROMACS forum.
- Badges
- Science topic