What could be the "physical significance" for the electrochemical circuit used to model EIS data ?

Hello, I have a two compartment electrochemical cell. I have put a nanoporous aluminum oxide membrane (nominal pore diameter = 20 nm) between these two compartments. Now I looked at the impedance...

10 November 2017 7,902 4 View

Is there a thermoresponsive liquid that does not mix with water?

Hello,I am looking for a thermo-responsive liquid which will not mix with water. The idea is to have two small connected reservoirs , one containing this liquid and the other having water. Then,...

11 December 2016 9,217 3 View

Can I use PRODRG for generating a GROMACS compatible topology file for a non standard nucleic acid?

My nucleic acid PDB file consists few non standard residues where the uracil, cytosine bases have been modified by adding methyl, phenol etc groups to them. Can I use PRODRG to generate a topology...

01 January 1970 1,823 3 View

How to measure the current flow across a membrane ?

Hello,I have an electrochemical cell consisiting of two chambers. These two chambers are separated by a membrane.Now, I want to observe the flow of current across this membrane for different...

01 January 1970 5,057 4 View

How to calculate the mean force from PMF values?

I have a Potential of Mean Force (PMF) values obtained against a reaction coordinate in a file. This was generated using a pulling molecular dynamics simulation. I am thinking of taking numerical...

01 January 1970 3,509 8 View

Is there a software tool for creating biomolecular structure for MD simulations ?

Is there any software tool to create the following : (1) DNA nulceotides with one S-H (thiol) group at its tail (2) To form an Au-S bond between the thiol and a layer of gold atomsI would like to...

01 January 1970 9,765 7 View

How to use make_ndx in GROMACS version 4.5.7?

I am using GROMACS version 4.5.7 and in my topol.top file there are 3 chains in the [molecules] section. Of these , two are protein chains. How can I use make_ndx to combine both the chains into a...

01 January 1970 8,410 2 View

How do I create a Au-S bond on a layer of gold in PDB format for use in MD simulations ?

I have created DNA and protein residues in Chimera for use in MD simulations. I would like to know about different ways to create a layer of gold atoms and a Au-S bond in PDB format so that it can...

01 January 1970 6,187 2 View

I have a PDB file in which many protein residues are missing and this produces an error when I use pdb2gmx (GROMACS) , what can I do to fix it?

The protein is missing many residue parts and when I used pdb2gmx with the -maxwarn function I found that the total charge on the protein was + 5.269 electron units. How can I go about in fixing...

01 January 1970 4,413 11 View

How do I add a new DNA residue to the terminus of my DNA PDB ?

I want to add a new DNA residue to the existing terminus of my DNA PDB file. How can I go about this task?? Can I use PyMol or Chimera ?

01 January 1970 4,987 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

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MGL tools

20 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 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