Is there a Gromacs Tutorial to add a residues to a force field and modifying a .rtp, .itp, atomtypes.atp and residuetypes.dat file?

If anyone have gromacs tutorial to a new residue to the topology. The protein which I am working on has 4 NAG (N-acetyl Glucosamine) and 1 ALS (2-amino 3-oxopropionic acid). These residues were...

05 June 2015 2,026 3 View

Why do I get huge fluctuations in RMSD when I simulate a protein in 20ns using Amber99sb force field in Gromacs 5.0.4?

02 March 2015 5,987 7 View

How to include the residues N-acetyl Glucosamine (NAG) and 2-amino 3-oxopropionic acid (ALS) in gromacs 4.6.5 version's topology ?

My protein has 4 NAG and 1 ALS residue in its sequence. When I tried to simulate the protein using gromos96 53 a6 force field , it's showing a fatal error as: residue 'ALS' not found in residue...

31 December 2014 5,993 4 View

How to install Tinker (Molecular design software) in ubuntu 14.04 version ?

11 December 2014 6,099 3 View

Can anyone tell how to install gromacs on Ubuntu 14.04 ?

I am using ubuntu 14.04 version, please tell me which version of GROMACS I have to use for this ubuntu 14.04 version. And give me the Installation steps. I have installed cmake and c++98 compiler.

11 December 2014 7,180 4 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

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

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 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

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View