How to carry out my experiment on lipid Membrane and Polymer simulation studies with gromacs?

I struck with generating topology for lipid membrane and polymer through gromacs. I tried different force filed like lipid force filed etc. I am unable to generate topology file through gmx...

05 June 2016 8,762 2 View

Can anyone help with setting PME grid dimensions?

I tried several values in this process pme_order = 8 / fourierspacing = 0.48 vs pme_order =10 / fourierspacing = 1.20 try comparing to the the default: pme_order = 4 / fourierspacing =...

04 May 2013 5,831 0 View

Protein-modeling tools.

I am modeling three structures using MODELLER, now I want to merge these three model structures to form a unique model. Can anyone suggest any open-source tools or online servers other than...

01 February 2013 3,452 0 View

How to model Homodimers

Can anyone tell me how to model Homodimer from target sequence through Modeller? It means A and B chain

01 February 2013 2,358 4 View

Biojava code for multiple sequences alignment and distance tree.

Using Biojava, I want to read multiple sequences and make an alignment for distance tree. I tried using cook book but I am getting an error, can anyone help me with this problem? import...

01 February 2013 1,029 3 View

Regarding .mdp file for GROMACS

Can anyone give me the best molecular dynamics parameters file for GROMACS?

01 February 2013 2,920 15 View

Error in MODELLER - merging structures.

I am modeling three structures using MODELLER, I am trying to merge these three model structures to form a unique model through but it is giving an error: rdpdb___303E> No atoms were read from...

01 February 2013 3,849 2 View

Is it possible to design a drug compound to suppress the mutation in the DNA?

Is it possible to design a drug compound to suppress the mutation in the DNA ,I have the logic to hold the drug at particular site in mutated DNA, am I right ?

08 September 2012 4,878 5 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