Gyration for a specific part of a protein?

Hey Guys, I have a ubiquitin, I am planning to claculate radius of gyration for residue 1 to 24 and 25 to 76. How can I make this? What command shall I use? Thank you. Maryam

11 December 2017 3,373 3 View

Warning message in gromacs for radius of gyration?

Hey Guys, I am calculationg radius of gyration for 1ubq. My reference file is a pdb file. and I cannot change it. So I have to deal with it!! The problem is that I receive 2 warnings: WARNING:...

11 December 2017 5,153 6 View

Unfolding in negative ion mode in gromacs?

Hi friends! I am running my simulations in negative ion mode, gromacs. The problem is that, my proteins completely unfold, and rotate badly. At the very begininng they start unfolding and...

10 November 2017 5,988 1 View

Unwanted rotation in gromacs?

09 October 2017 1,566 7 View

How to calculate radius of gyration using .gro files?

Hello! How can I calculate radius of gyration for the proteins using .gro files. We use .tpr and .xtc files to calculate R of G but right now I need to use my .gro files. Thank you.

07 August 2017 3,062 4 View

Combining100 .gro files to just one .gro file?

Hello friends! I have 100 .gro files. How can I combine them and create just one .gro file? Thank you! Maryam

07 August 2017 8,750 1 View

Buffer or additive for Mass spec in negative ion mode?

Hello friends, I am really really desparate right now! I am working in negative mode in Mass spec. I added formic acid+acetonitrile+water to my protein and I didn't receive any signal. I added...

02 March 2017 3,735 10 View

Paper or book about the relationship among salt bridge, protein, genetics and evolution?

Hello Friends, I look for a paper/book/website to study about the relationship among salt bridges / proteins/genetics and evolution. I have searched alot but I failed. Can you please advise me? Best,

01 February 2017 9,581 3 View

How to determine nterm only on central protein?

Hello everyone! I have 1 central protein in pymol with 6 surrounding proteins. I want to find a command to say: please select nterm only on central protein. How can I do this? Thank you.

01 February 2017 996 0 View

How to determine side chains which I have measured the distances between?

01 February 2017 9,159 9 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

How to increase a model accuracy ?

dear community, my model is based feature extraction from non stationary signals using discrete Wavelet Transform and then using statistical features then machine learning classifiers in order to...

03 March 2021 6,994 5 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

Why almost every element would be metallized in sufficiently high pressure and low temperature?

(This statement is from wikipedia, BTW). What is so special about metallic bond that is limiting high-P low-T state of a matter (as long as individual atoms exist, not white dwarf of neutron star...

02 March 2021 3,309 2 View

How to formulate Energy minimization in Molecular dynamics simulation for alloys using meam potential?

during MD simulation, the atoms are not moving as per required. The problem (as per my observation) lies in energy minimization technique. upon application of tensile strain in x or y direction,...

22 February 2021 380 5 View

Magnetismic Gravity in the universe?

MAGNETISMIC GRAVITY What is magnetism? Something magnetic has a + and - charge. If 2 + or - are pushed if + and - are pulled. But what is the main reason for this? Why does magnetism have a pull...

21 February 2021 9,538 3 View

Has anyone succeeded in capturing uranium atoms in a fullerene structure?

Additional questions are: What are the encapsulating atoms? How difficult was the process and what rates were achieved? What factors most seriously affect the economics?

20 February 2021 3,134 5 View

How to construct different filler shape in MD simulations?

Is there any way to construct different initial filler shapes like triangle, square, rectangle, pillar, and tube in any simulation software.

20 February 2021 1,750 1 View

How to get the vector of a specific vibration mode in phonon dispersion?

For example, I have this phonon dispersion(Fig. 1), and now I would like get vector of atoms which describes TA1 in P. I know v_sim can show vibrational animation of specific mode, but I do not...

20 February 2021 4,332 4 View

What are the potential shell well and atomic solvation parameters for the boron atom?

I have a protein-ligand docking project. The ligand contains boron atoms that are not detected by Autodock software. To solve this problem, it is necessary to introduce the boron atom to...

19 February 2021 1,236 1 View