German Sastre

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Questions related from German Sastre

What is the best way to obtain vibrational and rotational spectra from molecular dynamics simulations?

Vibrational and rotational spectra can be calculated from the molecular dynamics trajectories, but this task is, many times, performed by a different software than that employed for the MD.

12 December 2013 9,458 2 View

Protein-ligand interactions using molecular dynamics?

'molecule-1' binds to a pocket in a given protein, while 'molecule-2' does not bind. However, using MD, both molecules fit well in the active site (pocket). Why? I can only suggest that the...

11 November 2013 10,044 13 View

How to calculate pressure of an adsorbed gas in a microporous material using molecular dynamics?

Without a porous materials, gas molecules could be considered non-interacting (lets make this approximation) and hence knowing V,N,T, I can easily apply P=NRT/V and I obtain the pressure. Let's...

10 October 2013 4,481 4 View

Atomistic NVE MD run with temperature problem.

I'm running an atomistic MD simulation using the NVE ensemble. Unfortunately, the temperature does not stay constant throughout the simulation. To solve this problem I have checked the timestep...

03 March 2013 8,417 12 View

I'm looking for a free software to find molecules that overlap (not bind!) with a target molecule.

The software should work like this: I choose a molecule; and then the software scans a whole library of many many molecules, and then it quantifies the overlap of each one of them with my target...

01 January 2013 2,593 2 View