Do you know a good/fast tool to analyse protein-lipid interactions from a MD trajectory (GROMACS trajectory)?

I mean the number of contacts per protein residue with different different parts of the lipids. It more or less can be done in GROMACS, but you need to create many indexes for each trajectory, so...

10 November 2014 113 1 View

Problem inserting protein into a POPC bilayer?

04 May 2014 4,818 5 View

How can I do ensemble docking with Autodock Vina?

I want to do ensemble docking using different conformations of the receptor from MD with Autodock Vina? Is there any script available for such thing?

03 April 2014 638 3 View

Why do constraints equal all-bonds during production run?

03 April 2014 3,332 5 View

Have you ever had problems when loading .trr and/or .trj GROMACS trajectory files in VMD?

I'm a new GROMCS user. I've run an NVT equilibration of a explicitly solvated protein-ligand complex, I've extracted frames throughout the trajectory in both .pdb and .gro format and I've open...

02 March 2014 8,201 1 View

Is there any software or script to transform a coarse grained pdb file to atomistic without knowing the definition of the beads used in CG?

I've tried CG builder of VMD but it does not work

31 December 2013 4,332 2 View

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10?

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10? Since, the growth curve from day 2 to 10 won't be like the "Logistic curve" it might not follow logistic...

03 March 2021 1,401 3 View

After a reference from Int J Body Compos Res, can any body help?

Hi, I am after the reference below, my library says it cannot obtain a copy either locally or internationally, any help appreciated! Chris Wang ZM, Heshka S, Wielopolski L, Pi-Sunyer FX, Pierson...

03 March 2021 6,193 1 View

What techniques can I use to determine the miscibility of polymer blends?

The term miscibility refers to the single-phase state in thermodynamics. I do not mean the compatibility of different components. To determine the miscibility I know several techniques such as...

03 March 2021 4,107 4 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

Shall I skip the measurement model in SmartPLS?

Hello everyone, I had run a mediation model in SmartPLS using questionnaires that were already validated among my statistical population. A professor who edited my paper -though she is not...

01 March 2021 3,052 3 View

What is involved in morphological changes of SEM images of a substance?

In the sem analysis of CaCO3 nanaoparticles, the morphology images showed spherical shaped particles but the proposed morphology for these type of nanoparticles is trigonal. I prepared the...

01 March 2021 1,960 4 View

Joint behaviour in Abaqus is not captured well?

I am working on roof joint and trying to simulate the behaviour in Abaqus. I am successful in running the model but the final graph does not follow the experimental curve in the negative direction...

01 March 2021 6,661 3 View

Glass fiber content in a gypsum board ?

Any idea on how to get the volumic ratio of glass fiber in a gypsum board ? Thank you for your help !

01 March 2021 2,501 3 View

How to define tie constraint between rigid body and another part in dynamic explicit model of Abaqus?

Hi dear researchers I connected a rigid body into the part of my structure by tie constraint and then I added displacement to rigid body, in static general step every thing is fine and these two...

28 February 2021 3,442 2 View

What is the indication of the absence of peaks in Methanol electrooxidation CV curves ?

I have several question regarding the MOR; hope anyone help me better understand. 1- in CV using (KOH+MEOH) what is the indication of absence of the redox peaks? shouldn't they exist as a sign...

28 February 2021 4,851 8 View