How to restrain ligand/peptide in Protein pocket for NAMD?

09 October 2016 6,506 3 View

How can I find the lowest energy conformation of Protein-ligand complex after 10 ns simulation?

05 June 2016 816 9 View

What is the standard volume value in free energy of restraint?

i am calculating free energy of restraint for absolute binding free energy system of protein and ligand. i am confused between standard volume values. standard Volume is 1660A^3 , should i use...

04 May 2016 5,479 1 View

Can anyone help me in understanding REMD (Replica exchange Method) protocol in gromacs?

hi Researchers and Scientists i am working on Protein ligand binding free energy, i want to use Replica exchange method for complex simulation as well as ligand in water simulation, i have studied...

04 May 2016 5,434 3 View

Is there any rule for selecting atoms for distance restraints?

04 May 2016 1,548 3 View

Can anyone suggest me the beginner tutorial for calculating protein protein binding free energy using GROMACS?

04 May 2016 5,134 2 View

Free energy of restraints?

03 April 2016 4,472 0 View

Volume corresponding to the one molar standard state in Gromacs?

hi gromacs experts How can i find Volume corresponding to one molar standard state. background i have Protein-ligand complex simulation and i need to find energy of restraints which requires...

03 April 2016 2,995 1 View

Can we apply simple solvation free energy calculation simulation for ligand in water simulation in absolute binding free energy calculations?

Hi, all GROMACS specialists. I have a question about ligand simulation in water. In binding free energy calculations of ligand and protein, we need two simulation systems, one -protein+ligand in...

02 March 2016 8,975 5 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

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View

Why the results when using wall thickness and when using shell conduction are different in ansys fluent?

Actually, I am running cfd simulation for a heat exchanger which has two fluids one hot and other one is cold fluid. there is a solid domain between them, which I removed and instead I have used...

01 March 2021 9,537 2 View

Joint behaviour in Abaqus is not captured well?

I am working on roof joint and trying to simulate the behaviour in Abaqus. I am successful in running the model but the final graph does not follow the experimental curve in the negative direction...

01 March 2021 6,661 3 View

In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein?

Hi In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein? I got this error in the add-ion stage: Fatal error "./ amber99sb-ildn-HHH.ff / force...

01 March 2021 8,747 4 View