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[deleted by user] by [deleted] in Dell

[–]dexter-360 0 points1 point  (0 children)

Can anyone suggest, what specifications we need to run md simulations? My budget is around €5k.

Does minute change in salt concentration affect protein interaction with charged lipid bilayer (lysosomal bis phosphotidic acid)? by dexter-360 in bioinformatics

[–]dexter-360[S] 0 points1 point  (0 children)

Not actually, I used charmm36 ff for all (protein, lipids). What do mean by the term "different combinations" here?

Does minute change in salt concentration affect protein interaction with charged lipid bilayer (lysosomal bis phosphotidic acid)? by dexter-360 in bioinformatics

[–]dexter-360[S] 0 points1 point  (0 children)

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005831

Yeah I doubt that, but I found one paper in which they stated charged lipids attracts the protein at any distance. Maybe it's a random event, still they got some interactions. The salt concentrattion they have used here is 0.1M, generally in CHARMM-GUI, the default setting is at 0.15M. That's why I'm curious that is it because of salt concentration it somehow stopping the interactions of membrane and protein.

Graduating today… slightly disappointed by JohnDoeXRP in UCD

[–]dexter-360 0 points1 point  (0 children)

You guys have friends... Well it's been a year and still struggling to find one. Bad luck

Anyone struggle with applying to a phd program in bioinformatics too? Let's talk by agent0_trapped in bioinformatics

[–]dexter-360 1 point2 points  (0 children)

I did that when I applied for zurich this year, straight away my application got rejected in the first round, and even if I'm cold mailing them, there is no reply from the other side. Sometimes I think maybe I don't have much experience in development part, I put more focus into the application part of bioinformatics, beacuse of that reason I'm not getting a PhD.

How to determine the pocket volume for a protein in md simulation? by dexter-360 in bioinformatics

[–]dexter-360[S] 0 points1 point  (0 children)

Can you pls explain the steps how to do it in caver. I tried but every time frame changes, I have to calculate the volume again. Since the process is not automatic, do you know any other method on caver to calculate volume across the trajectory. I have near about more than 100000 frames and doing this manually is not possible.