How to check whether the protein bind first or the membrane using MD simulation?

I have a system with two proteins and a membrane as following protein-1, protein-2, and membrane bilayer. I would like to know whether the protein-2 binds first to protein-1 or the membrane to...

06 July 2018 9,903 1 View

How to validate a homology model?

I would like to validate a homology model. After peroforming MD simulation, one way is to check the stereochemical quality, Ramachandran plot, dssp, B-factor, etc and map the model with the...

06 July 2018 6,108 11 View

How to set gradient background in VMD in .vmdrc file?

I would like to set the default background in vmd as gradient. Therefore I tried the following method to set default background gradient in ~/.vmdrc file but that did not work. Could anyone please...

05 June 2018 9,681 2 View

Problem with VMD 1.9.2 in Ubuntu 16.04 when the representation changes to new cartoon

I have installed VMD 1.9.2 on Ubuntu machine and when I try to change the representation from lines to cartoon the GUI becomes very slow and one can feel like VMD is not working. It does not slow...

07 August 2017 495 10 View

What could be the correct 3 letter code for sulfonated tyrosine?

Is there anything like universal 3 letter code for sulfonated tyrosine like other usual amino acid residues

07 August 2017 4,076 2 View

Regarding hydrogen bond analysis in GROMACS?

07 August 2017 1,392 4 View

VMD movie making of GROMACS trajectories?

While making movie of GROMACS trajectory in VMD, How one can stop motion of protein going from one direction to the other in PBC box?

08 September 2016 8,120 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View