Molecular Dynamics of Arsenic ligand with protein?

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Problem in adding other molecule in system for molecular dynamics

Hello all, i am working on a protein complex. For a certain analysis, i am trying to add ethylene molecule in system (Protein + water), to check the variation in system. I have inserted 10...

06 July 2017 8,630 4 View

Gromacs error while mdrun

Hello all, i am working on a protein complex. I have opted simulation analysis for some specific analysis of my complex. For which i have generated a system for complex in water having 10...

05 June 2017 6,333 0 View

How to define option in g_rms in PBS file

Hello everyone, i am working on gromacs tool (V 4.6.5). Server, in which we work, accepts PBS for job runs. I have prepared my .tpr file on local machine and performed the mdun on server. As my...

04 May 2017 8,569 12 View

I am working on DNA-protein complex MD in gromacs, how ever stuck on a step where in grompp step getting 'Fatal error: No such moleculetype DNA' ?

I am interested in DNA-protein MD. I have a custom made structure of a DNA motif, i have edited it (from ATGC to DA, DT, DG, DC) for gromacs and generated topology using amber99sb-ildn.ff. After...

01 February 2017 1,826 5 View

i want to use simbiology feature of MATLAB software for system biology simulation ...but have no idea about filling the compartments of it and the RUN...

i want to use simbiology feature of MATLAB software for system biology simulation ...but have no idea about filling the compartments of it and the RUN(simulating) the model programming.... please...

08 September 2011 5,058 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

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

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

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

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

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