Can I do PCA for a particular domain of a protein?

I am trying to do PCA from the MD trajectory of a multi-domain protein using GROMACS tools. I am using gmx covar and gmx anaeig for PCA. My protein has many domains, but I would like to focus on...

11 December 2019 996 4 View

How to unwrap using PBC unwrap?

03 April 2019 1,832 4 View

Is it possible to continue the MD run?

After about 600ns of my MD run, I notice that my molecule has started interacting with the image. I understand that I should use a larger box length but is it possible for me to continue the MD...

02 March 2019 2,749 4 View

How to do a continuation run in GROMACS 2018 with new file name?

I am running MD simulations with GROMACS 2018. I am planning to run 500ns but I want my trajectories and other output files in five different sets, i.e., filename XXX_100ns. , XXX_200ns.,...

01 February 2019 6,542 4 View

How to add atoms to the mass database in amber14sb_parmbsc1 forcefield?

I am using GROMACS2018 with amber14sc_parmbsc1 force field for simulations. I have DNA,RNA,protein,NA,MG and water in my system. I want to analyze my trajectory. the way I have written my...

31 December 2018 7,232 3 View

How to calculate distance using gromacs?

I have two groups defined in the index file. The group [ protein ] has all protein atoms and the group [ DNA_5 ] has all the atoms of residue id 5 of DNA. I want to calculate the distance between...

09 October 2018 1,648 5 View

How to plot the histogram.xvg file obtained from GROMACS REMD?

I am having difficulty in plotting the histogram.xvg file obtained from REMD using xmgrace. Can I plot it with matlab? if yes please help.

09 October 2018 6,952 1 View

Why is gmx genion with - neutral option not adding appropriate no. of ions?

My systems contains proteins + Nucleic Acids + Mg2+ ions. First I solvate this using gmx solvate and then I try to neutralize the system using gmx genion with the option "-neutral". However, I see...

03 April 2018 7,791 3 View

Why after energy minimization by gromacs (steep) a bond in a particular aa residue is broken or the dist bet two atoms in that aa becomes ~3A or more?

I am attaching here two files: 1. XXX_solv_ions.gro : This file was used for energy minimization and the residue (VAL 647) seems perfect here 2. em.gro : This file as obtained after energy...

02 March 2018 2,546 1 View

Issue with "wrap/unwrap" in GROMACS

I have performed MD simulation with RNA (3 strand helix) using GROMACS. During MD-run the strands are separated due to PBC and also broken during PBC. How to "unwrap" or make the molecule...

04 May 2017 6,424 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