How do we do micelle clustering and how do we make index file for molecules in micelles?

My system contains three micelles. I want to calculate radius of gyration for each micelle in the system. I did the micelle clustering, but I am struggling with the step 3 in...

07 August 2018 2,635 1 View

How can I model a hexagonal phase using Packmol?

Dear All, I want to arrange my surfactant molecules in a hexagonal arrangement for my MD simulation. Appreciate, if anyone can guide me to do that. Thank you.

06 July 2018 8,423 2 View

How to solve the Gaussian error; Water molecule starting at atom 93528 can not be settled?

Dear All, My system contains water molecules and polyethylene glycol molecules. I generated the box (15.2*15.2*15.2 nm*3) using genbox command. Thereafter, PEG molecules were added using gmx...

09 October 2017 7,074 0 View

What should I assign to pcon and ncon in polar.mdp in g_mmpbsa?

Dear All, In my MD simulation I only added counter ions (20 Na+ ions) to neutralize the system. Now I want to do MM_PBSA calculations for my MD runs using g_mmpbsa. In order to do perform polar...

06 July 2016 7,537 1 View

Can we do molecular docking in the presence of crystallized water molecules using DOCK6?

Dear All, I want to do molecular docking processes for an enzyme and ligands in the presence of co-crystallized water molecules (of the enzyme) using DOCK6. Can anyone help me? Appreciate if...

05 June 2016 2,615 0 View

How to get publication quality images in PoseView?

Dear All, I want to get high quality images of 2D pictures generated by PoseView software. Can anyone help me? Thank you.

05 June 2016 6,125 1 View

How rmsf of linker doamin in human topoisomerase I change with the binding ligand?

Dear All, I completed molecular dynamics for three ligands, T1L25, T2L25 and T3L25 using GROMACS software with CHARMM27 force field. How can I explain the rmsf behavior of linker domain (linker...

03 April 2016 5,113 5 View

Ligand interactions with DNA

Dear All, I have two receptor-ligand complexes. In one system, the ligand intercalates in DNA and from two hydrogen bonds (one with the enzyme and one with DNA duplex). In other system, the ligand...

02 March 2016 329 4 View

How can I use the itp file generated from SwissParm for MD simulation using GROMACS?

Dear All, I used SwissParm to generate CHARMM itp files for my ligand molecules. I used GROMACS for molecular dynamics simulations. After getting the itp file for the ligand, I used that file...

11 December 2015 3,606 0 View

How can I get topology file for my ligand molecule?

Dear all, Currently I am trying to do molecular dynamics simulations for human topoisomerase I enzyme. I am using GROMACS software with CHARMM forece field. I want topology file for my ligand...

10 November 2015 6,680 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

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