How to add extra molecules in MD simulation?

Dear researcher, I want to simulate my protein with the denaturants (MW-139 Da). I am using Gromacs 2018.2 version and the extra molecules were added by using gmx insert-molecule command. I want...

01 February 2019 1,509 3 View

Too many LINCS warning?

Dear researcher, I want to simulate my protein in different concentrations of Guanidinium chloride. I successfully added 4M GdnHCl in a cubic box. But when i want to neutrilize the system with the...

10 November 2017 9,007 0 View

How to simulate selenium containing enzyme in Gromacs?

Dear researcher, I want to simulate a selenium containing enzyme. But when i processed the selenium containing enzyme using pdb2gmx command so it is showing an...

09 October 2017 6,044 11 View

About free energy landscape calculation using Gromacs?

05 June 2017 4,631 5 View

How to predicted the Stable structure from MDS?

02 March 2017 7,404 6 View

Please provide me urea.gro and urea.itp files for MDS?

01 February 2017 7,836 4 View

About mm-pbsa calculation?

11 December 2016 5,709 6 View

About diamer dissociation from MDS study?

10 November 2016 8,445 5 View

About the cross correlation matrix?

10 November 2016 7,169 0 View

About Principle Component analysis or Essential dynamics?

Dear researcher I am facing a problem in principle component analysis. I calculated the eigenvalue by g_covar command. After that i saw in many Literaturrates they give the percent value. In...

09 October 2016 4,751 4 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