How to get hydrogen bond analysis using MDAnalysis working with custom atom names?

Hi, I'm up against a horrible deadline so I'm hoping for some help figuring out what I'm doing wrong. I have a list of custom atom names in Gromacs of which I want to perform hydrogen bond...

31 December 2019 8,270 5 View

How to add periodic rendering in PyMol?

I have a licensed copy of PyMol (ver 2.3.1) and I am looking to 'replicate' a protein/bilayer i.e., in VMD you select "Periodic" and select from a number of x, y and z options. This, in turn,...

11 December 2019 7,494 4 View

How to resolve GROMACS mdrun seg fault during minimisation?

I'm waiting on email conformation for the GMX user group, but this is in reply to Reviewers so I'm pressed for time and asking here. I'm building a small collagen-based system. The crystal...

10 November 2019 4,275 8 View

How do derive force constants from QM into MD for drugs and small compounds?

Hi, I know the fundamentals, I'm would like an update on the available open-source software. I have a set of small molecules and drug molecules. I've derived their ground state structure using...

10 November 2019 9,586 3 View

How to increase the number of optimisation steps in ORCA?

What is the keyword to increase the number of optimisation steps (not the number of SCF steps) in an ORCA optimisation calculation? The warning is suggesting I increase the "number of...

08 September 2019 1,843 2 View

Are these QC DFT settings appropriate?

I'm picking up quantum chemistry after a three year break. I've forgot a lot and I'm now using ORCA (version 4.0.1.2). My system is a non-enzymatic chemical reaction between lysine, arginine...

07 August 2019 1,651 3 View

Looking for CHI (transmembrane modelling software)?

I am looking for an old piece of software called CHI. It was used to model protein transmembrane domain interactions in a gas phase. I believe it was part of...

01 February 2019 5,274 2 View

How to change the amino acid in a Gromacs topology and force field file?

Hi all. A similar question to this has been asked several times, however there is subtle difference. I would like to change e.g., an alanine to a glycine (or any amino acid) in a .gro file AND...

11 December 2018 677 11 View

How to calculate whether a disease outcome in a population is by chance or significant?

Hello all, I have a huge dataset of longitudinal medical records. Each record contains indications for drug and disease. I have been able to calculate the Cure Rate in the population given a...

09 October 2018 2,092 5 View

How to determine whether two time-series trajectories are significantly different?

I have six time-series plots as a measurement of some soft-matter physical function F(t), see the graph below. In most instances, it is quite clear that particular variations in the property of...

08 September 2018 418 8 View

error in running a model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

error in modelling model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

MGL tools

20 June 2021 0 0 View

i have some problem with chtMultiRegionSimpleFoam

--> FOAM FATAL ERROR: Maximum number of iterations exceeded From function Foam::scalar Foam::species::thermo::T(Foam::scalar, Foam::scalar, Foam::scalar, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar) const) const [with Thermo = Foam::hConstThermo >; Type = Foam::sensibleEnthalpy; Foam::scalar = double; Foam::species::thermo = Foam::species::thermo >, Foam::sensibleEnthalpy>] in file /home/ubuntu/OpenFOAM/OpenFOAM-4.1/src/thermophysicalModels/specie/lnInclude/thermoI.H at line 66. FOAM aborting #0 Foam::error::printStack(Foam::Ostream&) at ??:? #1 Foam::error::abort() at ??:? #2 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::calculate() at ??:? #3 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::correct() at ??:? #4 ? at ??:? #5 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6" #6 ? at ??:?

24 March 2021 0 0 View

Could you recommend any books about Number Theory?

Beginner level books. High level books. Analytical Number Theory. Algebraic Number Theory. Combinatorical Number Theory. Books about partitions. Books about primes.

03 March 2021 7,174 5 View

Resistor definition in Piezoelectric bimorph with ANSYS workbench

Hello, good day! I am trying to simulate similar bimorph piezoelectric harvester with below commands. However, the output power doesn't change with resistor value. Please help to find the reason. ET,10,CIRCU94,0 !SET UP RESISTOR R,1,100000 !RESISTANCE VALUE TYPE,10 !SET ELEMENT TYPE E,1,2 !CREATE RESISTOR BETWEEN NODES 1 AND 2 Thanks in advance Regards,

02 March 2021 0 0 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

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

How to classify strictly upper triangular matrices by similarity?

Let F be a field. Consider U, the set of n times n strictly upper triangular matrices in F. For X, Y in U, we call them similar if there exists some S, which is non-degenerate and upper...

01 March 2021 2,957 8 View

Is CD44 degraded in lysosome together with hyaluronan after CD44 mediated endocytosis of hyaluronic acid?

Also when RHAMM binds hyaluronic acid, they get internalized, will RHAMM also be degraded? Or both CD44 and RHAMM will be transferred back to the cell membrane? Asking for breast cancer cell line...

01 March 2021 8,169 2 View