I got some questions that might be too basic or completely wrong.
1) To perform GaMD is necessary to first obtain a series of parameters that will be later written in the gamd-restart.dat and then start a new simulation from there?
2) I got a big system (1400 residues, membrane protein with disordered regions) but I have very low values of K0P and K0D .... in your paper you mentioned that the chingolin was stable at 0.17 K0D but I was wondering how you measure the stability of the system? RMSD?
3) In the Gamd.log sometimes I got very high values in the last two columns (Boost-Energy-Potential,Boost-Energy-Dihedral). Is there a threshold I should never trepass? Or this depends on the system size?
4) GaMD could potentially be combined with Markov State Models analysis?
5) On a very basic level, how I decide to switch between iE=1 and 2 ?
Best,
Dr Alessandro Barbieri
The University of Manchester
BII A* STAR Singapore
Last edit: Alessandro Barbieri 2022-06-24
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello,
I got some questions that might be too basic or completely wrong.
1) To perform GaMD is necessary to first obtain a series of parameters that will be later written in the gamd-restart.dat and then start a new simulation from there?
2) I got a big system (1400 residues, membrane protein with disordered regions) but I have very low values of K0P and K0D .... in your paper you mentioned that the chingolin was stable at 0.17 K0D but I was wondering how you measure the stability of the system? RMSD?
3) In the Gamd.log sometimes I got very high values in the last two columns (Boost-Energy-Potential,Boost-Energy-Dihedral). Is there a threshold I should never trepass? Or this depends on the system size?
4) GaMD could potentially be combined with Markov State Models analysis?
5) On a very basic level, how I decide to switch between iE=1 and 2 ?
Best,
Dr Alessandro Barbieri
The University of Manchester
BII A* STAR Singapore
Last edit: Alessandro Barbieri 2022-06-24