Water flux inside a pore?

Hi all, I am performing a Molecular Dynamics simulation of a water pore inside a membrane. I am experimenting with some analysis options and I am having a bit of a trouble understanding the water...

01 February 2019 8,849 2 View

Trouble with gmx distance?

Hi, I am trying to calculate the distance between two atoms, which are defined in an index file. The command that I use is: "gmx distance -f output.gro -s prod.tpr -n index.ndx -oav...

07 August 2017 3,238 4 View

How are the default parameters derived?

Hi, the default values for bonds, angles like kb, b0 etc, how are they calculated?

01 February 2017 5,246 2 View

Temperatures for Replica Exchange Simulations?

Hi, I am trying to simulate a protein using Replica Exchange. By reading at the literature I found what values are needed as a Tmin, Tmax and also the number of replicas. Apart from that there is...

07 August 2016 7,329 1 View

Paper for Replica Exchange MD?

Hi I want to perform an remd simulation of a large protein system. The bibliography I found so far is about small systems and doesn't describe the way they decide on the number of replicas or the...

07 August 2016 3,321 8 View

How to calculate bond force constant for CLA for molecular dynamics ?

I am using Gromacs and I want to edit the ffbonded.itp in oplsaa.ff directory. I have by literature the bond length but I can't find the force constant. Is there a way to calculate it?

05 June 2015 1,829 5 View

Any advice on my problem adding new molecule in aminoacids.rtp - gromacs?

04 May 2015 8,571 4 View

How can I proceed with a molecule.itp in Gromacs?

I have made a molecule.itp file according to the chapter 5 of Gromacs Manual and existing entries in the ff directory I want to use.My problem is that I don't know how to continue, in theory I...

04 May 2015 5,387 3 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

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

I got 02 moderator values defining Johnson-Neyman significance regions. Is it an error?

Hi everyone, I am conducting research for my Master's thesis. I am using PROCESS by Johnson-Neyman to analyze my Moderator model. I test the relationship between Public Service Motivation and...

03 March 2021 2,350 2 View

Do I need to do linear regression before running mediation analysis using PROCESS MACRO by Hayes ?

I just wanted to check if I need to run a linear regression separately if I am using PROCESS MACRO to run mediation analysis. Thank you.

02 March 2021 4,359 3 View

Do I need to strip the PVDF membrane before staining it with colloidal gold?

Dear Colleagues, After running Western blot on PVDF membrane and detection using ECL, I would like to stain my PVDF with colloidal gold to be able to allign the ECL image with total proteins on...

02 March 2021 7,829 3 View

PACYC PCR not working after several attempts. Would anyone have any suggestions?

So, I have been trying to run a pACYC PCR which will be used later on for a Gibson Assembly. However the PCR is not working. I have already tried gradient PCR and changing extension time; however...

02 March 2021 1,146 2 View

What SPSS analysis should I run with one IV (with two levels) and two DVs?

Hi, I am trying to figure out which test would be most appropriate to run for the following question: Is there a difference in task blood pressure between smokers and non-smokers? There are two...

01 March 2021 8,235 2 View

How can I integrate a routing protocol in a tiny device (e.g. Raspberry Pi)?

Hi Community, I'm facing the issue of integration/compiling a new routing protocol in a WSN simulator. The final goal is to successfully add, configure this routing protocol in hardware devices...

01 March 2021 9,332 6 View

OpenBCI eeg--has anyone used them?

I'm looking to try out an off-the-shelf EEG set for some exploratory work. Curious if anyone has used the OpenBCI, and how much set-up work is required. I've heard they are more difficult to get...

01 March 2021 4,128 3 View

In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein?

Hi In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein? I got this error in the add-ion stage: Fatal error "./ amber99sb-ildn-HHH.ff / force...

01 March 2021 8,747 4 View