Dheeraj Prakaash

4 Questions 39 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 5,183 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 4,487 3 View

Phase transition temperature of PIP lipids?

Can anyone point me to a paper which states the transition temperature of PIP lipids, more specifically PI(4,5)P2? I want to know the approx temperature below which PIP lipids enter gel phase. I...

09 April 2020 2,010 0 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 6,225 1 View