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

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

How the parameters (such as Mw, Chemical bonds, polymer bland and so on) affect the mechanic property of polymer (such as storage, loss modulus) ?

Anyone can recommend any books on such topics? Thanks in advance.

02 March 2021 8,457 2 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 can you bring two structures together to create an adhesive bond in LAMMPS?

I have created an Ice 1h crystalline structure and an Aluminium substrate structure and equilibrated both at 250K. Now I need to bring them together in a way that an adhesive bond is created....

01 March 2021 3,325 2 View

What is the difference between genotype and haplotype data in the ped format?

Hi everybody In the ped format for genotype, alleles of any SNP are represented by two columns (one for each allele, separated by a space). Is a column sufficient for the haplotype to...

27 February 2021 1,965 1 View