Gromacs 5.1.4 installation errors

I followed the below instructions to install Gromacs-5.1.4 after patching up with plumed. and then ran gromacs-plumed simulations end up with following errors. I didnt see any errors, while...

07 August 2017 8,550 0 View

How to convert Xplor distance restraints to gromacs format or amber for rna ?

02 March 2015 4,425 3 View

How to plot the interface area plot along the trajectory of Gromacs MD simulation for the protein-protein complex ?

We did the Gromacs MD simulation for the protein complex , the complex is stable during 15 ns Simulation. We would like to plot the interface area plot for the protein complex along the entire...

11 December 2013 10,015 6 View

How to measure the binding affinity using fluorescent ligand with protein?

Could anyone provide references or protocols to measure the binding affinity by using fluorescent ligand with protein? Ligand shows fluorescence excitation/emission: 270/340 nm.

10 November 2013 2,928 10 View

How to set up unrestrained MD simulations on gromacs for protein-protein complex?

I would like to setup unrestrained MD simulations on gromacs for protein-protein complex . The protein complex was calculated by HADDOCK by using NMR Chemical shift restraints? Could you please...

02 March 2013 8,411 2 View

How to calculate the number of water molecules present on the binding interface of a protein complex ?

I would like to calculate the number of water molecules replaced before and after complex formation on the binding surface? How we can do this? Any suggestions?

11 December 2012 4,174 8 View

Moleculer dynamics simulations for Protein-Protein complex

I am new to MD simulation for Protein - protein complex , sorry for asking some basic questions ! 1. What Kind of information it will provide if I do MD simulation for protein complex after...

09 October 2012 9,837 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