Please anyone to help in preparing qm/mm input files by "namd" (Molecular Dynamics software) for a ligand-enzyme complex?

Hi All, I'm trying to prepare qm/mm files for a ligand bound to an enzyme, I followed the tutorial of "vmd" and "namd", but it still reports an error in qm calculations. Any idea please? Best,

08 September 2018 808 0 View

Can anyone please help in finding the Fourier transform of the distance equation?

Can anyone please help in finding the Fourier transform of the distance equation? The distance equation is: (Z2-Z1)2+(Y2-Y1)2+(X2-X1)2=D2 X1,Y1,Z1 are the coordinates of the first point. X2,Y2,Z2...

04 May 2017 131 3 View

I need simple executable to perform steepest descent minimization for protein structure (pdb)?

Hi all, I need simple executable to perform steepest descent minimization for protein structure (pdb), with instruction how to do it? Thanks,

10 November 2016 7,700 1 View

How to Call NAMD Molecular dynamics software from *.bat file on windows?

09 October 2016 7,401 0 View

Can anyone please explain if there is any software to produce coarse-grained 3D structure for RNA and DNA?

05 June 2016 3,303 5 View

Where can I find forcefields for phosphoserine to use with "NAMD"?

05 June 2015 7,007 6 View

With NAMD, where can we find standard config files for minimization, heating, equilibration,and production for all types of ensembles (NVE,NVT,& NPT)?

With NAMD, Where can we find standard config files for minimization, heating, equilibration, and production for all types of ensembles (NVE,NVT,& NPT)?

02 March 2015 6,106 4 View

In Molecular dynamics, which ensemble is better to use: NVE or NVT?

We use different ensembles in MD, which one is preferred to use?

02 March 2015 7,295 14 View

How can we solve the problem of energy drift in NVE ensemble in Molecular Dynamics?

How can we solve energy drift problem in NVE (constant energy, constant volume, and constant number of particles) ensemble in Molecular Dynamics?

02 March 2015 1,207 3 View

In Molecular dynamics (NVE), is energy drift of about +5 Kcal/mol.ns acceptable?

In Molecular dynamics (NVE ensemble), is energy drift of about +5 Kcal/mol.ns acceptable?

02 March 2015 3,680 2 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

Chlorinated organic formation in odor control scrubbers using hypochlorite?

I'm involved in a study of odor control technologies for municipal wastewater treatment plant. One of the control options involves a chemical 2-stage (acid/alkaline) packed bed scrubber. The...

03 March 2021 3,661 2 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

What solvent can I used for Paal Knorr reaction between 6-amino hexanoic acid and 2.5 hexanedione?

I am try to make the Paal Knorr reaction between 2.5 hexnedione and 6-amino hexanoic acid, my problem is type of solvent to use, because 6-hexaminohexanoic acid is soluble in water but I am not...

02 March 2021 4,443 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 to calculate average trend in maximum annual NDVI from MODIS?

I am wanting to calculate the average trend in maximum annual NDVI in Iceland from 2010-2020 using MODIS MYD13Q1 V6. How would I do this? I have currently inserted the NDVI bands from the MODIS...

02 March 2021 752 2 View