How can I determine the protonation state of a phosphorene sheet in acidic and neutral pH conditions?

Dear experts, I am going to perform an MD simulation on a system including water and phosphorene sheet in different pH conditions (low and neutral pH). However, I do not know if the different pHs...

11 December 2018 2,482 0 View

How to create a topology file for a receptor-ligand system?

Dear experst, I have got the .itp and .gro files for a drug and a nanosheet from a paper. Then I made the posre file for them using the genrestr command and performed MD simulations on them...

09 October 2018 8,396 6 View

WARNING: Listed nonbonded interaction between particles X and Y at distance ... can anyone please help me with this problem?

Dear all, I am trying to perform free energy calculations of a small drug in octanol using the GROMACS 5.1.3 software. I built a box of octanol using the following command gmx insert-molecules -ci...

02 March 2018 148 0 View

How to find the proper parameters for MM-PBSA calculations using g_mmpbsa package?

Dear experts, I need to perform MM-PBSA calculations using g_mmpbsa package. My problem is that how to determine proper parameters for .mdp file. for example Solute dielectric constant (pdie) or...

05 June 2017 6,663 3 View

How to determine the time needed for each window in umbrella sampling?

Dear all, Is there any criteria to determine the optimum run time for each window in umbrella sampling? My receptor has equilibrated after 30 ns of MD. Should I consider the same run time for each...

10 November 2016 614 4 View

What is the best approach to determine box size in an umbrella sampling simulation using Gromacs software?

Dear all, I want to perform PMF calculations on a protein-ligand complex and I am following the Gromacs tutorial. I am using Gromacs 4.6.5. But, I do not know how to find the best box size so that...

10 November 2016 3,613 5 View

What is the reason of blowing up a system in a simulation?

Dear all, I am performing a MD simulation on a branched polymer through GROMOS 53A6 force field. But, I don't know why when I execute the energy minimization, the system blows up. I have attached...

08 September 2015 9,624 4 View

What is the best Force Field for MD simulations on Drug-Dendrimer systems?

Dear all, I'm looking for a proper Force Field for MD simulations on Drug-Dendrimer systems. Could you suggest a good FF for this reason? It is mentionable that Im working with GROMACS software.

01 February 2015 9,119 3 View

How can I understand the umber of ligands can dock into a receptor?

Hi,I want to dock a ligand into a receptor with AutoDock Vina software, Is there any way to understand how many ligands can dock into a receptor, ifwe do not have any experiment date?Best...

31 December 2014 9,627 7 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

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

Why Austenite grains in steel show much more twinning than ferrite grains?

It is oftentimes said to be a distinctive metallographic trait that differentiates a fully austenitic and a fully felly ferritic steel without etching that might distinguish between two. Why...

02 March 2021 728 2 View

Is there a powerful system for the security of the systems distributed on IoT systems?

Is there a powerful system for the security of the systems distributed on IoT systems?

02 March 2021 3,858 10 View

How Relativistic effects is one reason for lanthanide contraction?

The Lanthanide contraction which is the decrease in ionic radii of the elements in the lanthanide series from atomic number 57, lanthanum, to 71, lutetium, is due to poor shielding of the 4f...

01 March 2021 2,272 4 View