Dheeraj Prakaash

3 Questions 30 Answers 0 Followers

Questions related from Dheeraj Prakaash

In Gromacs, is it necessary to set 'gen_vel = yes' (production.mdp)? I set it to 'no' and my simulations seem fine. What's the difference?

According to the gromacs manual, setting 'gen_vel = yes' for production generates initial velocities for particles, and setting it to 'no' doesn't. I set it to 'no' and my simulations still work...

12 March 2021 5,098 9 View

Steered molecular dynamics - Constant velocity - Gromacs: Can the imaginary object/atom (to which the spring is attached to) pass through the PBC?

Is it possible that the imaginary object/atom (to which the spring is attached, and which moves at a constant velocity - shaded in grey in the image) passes through the PBC? If it does and appears...

09 March 2021 4,407 3 View

Can I have your opinions on which are the 5 best tools/platforms for prediction of protein transmembrane structure (ranked 1-being best to 5)?

I retrieved a sequence of a receptor protein from Uniprot, and am currently using PSIPRED, TMHMM and Uniprot to compare their transmembrane (TM) predictions of the protein. But I want to ensure if...

04 February 2019 6,114 1 View