How can I make a decision among AutoGrid, AutoDock, LAMMPS and AMBER for MD simulation of DNA?

More Lan Mei's questions See All

Why does my DID stain some organelles besides the cellular membrane?

I stained MCF-7 breast cancer cells with DID following the manufactorer's protocol (20 nM for 20min). However, it is found out that some organelles were stained besides the cellular membrane. I'm...

09 October 2019 475 5 View

How to deal with mycoplasma in cell cultures?

How to deal with mycoplasma contaminant in cell cultures? The growth of my cells was obviously hampered.

07 August 2019 7,333 3 View

Dose EDTA influence the cell internalization of nanoparticles?

I am focusing on the cellular uptake of some nanoparticles. These particles can only stably exist in buffered systems containing EDTA. It has been reported that EDTA influence the permeability of...

06 July 2019 3,791 1 View

How to sterilize liquids (containing thermal unstable components) with really small volume?

I am testing antibacterial properties of a peptide of which the mass is as low as tens of microgram. If I want to set a wide range of concentration, I have to dissolve the peptide powder in a...

04 May 2019 690 2 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

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

Dear all, I was wondering if anyone knows whether MGLtools and Autodock can run on Mac OS?

I have tried to download the 64-bit version of MGLtools however, as many times as I have downloaded and uninstall the programs, an error arises that the app needs to be updated. Thank you.

03 March 2021 5,997 2 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