Water flux inside a pore?

Hi all, I am performing a Molecular Dynamics simulation of a water pore inside a membrane. I am experimenting with some analysis options and I am having a bit of a trouble understanding the water...

01 February 2019 8,849 2 View

Trouble with gmx distance?

Hi, I am trying to calculate the distance between two atoms, which are defined in an index file. The command that I use is: "gmx distance -f output.gro -s prod.tpr -n index.ndx -oav...

07 August 2017 3,238 4 View

How are the default parameters derived?

Hi, the default values for bonds, angles like kb, b0 etc, how are they calculated?

01 February 2017 5,246 2 View

Problem running heme proteins on gromacs?

Hi I am trying to simulate a protein containing a heme, using Gromacs and Charm27 force field. When I try to run pdb2gmx I get an error. I have looked the force field directory and found that this...

09 October 2016 2,942 2 View

Paper for Replica Exchange MD?

Hi I want to perform an remd simulation of a large protein system. The bibliography I found so far is about small systems and doesn't describe the way they decide on the number of replicas or the...

07 August 2016 3,321 8 View

How to calculate bond force constant for CLA for molecular dynamics ?

I am using Gromacs and I want to edit the ffbonded.itp in oplsaa.ff directory. I have by literature the bond length but I can't find the force constant. Is there a way to calculate it?

05 June 2015 1,829 5 View

Any advice on my problem adding new molecule in aminoacids.rtp - gromacs?

04 May 2015 8,571 4 View

How can I proceed with a molecule.itp in Gromacs?

I have made a molecule.itp file according to the chapter 5 of Gromacs Manual and existing entries in the ff directory I want to use.My problem is that I don't know how to continue, in theory I...

04 May 2015 5,387 3 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