How to use charmm36m forcefield with GROMACS?

I am planning to do MD simulation of IDPs using charmm36m force field. The software I am planning to use is GROMACS 2019. Hence, my question is how do I get the charmm36m force field in GROMACS...

01 February 2020 2,434 3 View

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

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

MGL tools

20 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

Resistor definition in Piezoelectric bimorph with ANSYS workbench

Hello, good day! I am trying to simulate similar bimorph piezoelectric harvester with below commands. However, the output power doesn't change with resistor value. Please help to find the reason. ET,10,CIRCU94,0 !SET UP RESISTOR R,1,100000 !RESISTANCE VALUE TYPE,10 !SET ELEMENT TYPE E,1,2 !CREATE RESISTOR BETWEEN NODES 1 AND 2 Thanks in advance Regards,

02 March 2021 0 0 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

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

What are the new 2D nanomaterials were used for Silver nanoparticles stabilization?

In the stabilization of AgNPs are vital in current research interest. However, some of the 2D nano-materials like graphene oxide, MoS2, etc... previously used to stabilize it. But still they shown...

01 March 2021 2,207 3 View

1 nm thick MgO thin-film to be deposited on Si wafer using thermal evaporation. What will be the optimum deposition conditions?

Favourable conditions of base pressure, rate of deposition. Also, by which characterisation technique to be used to verify the thickness of the deposited film.

28 February 2021 3,640 3 View

What is the difference between genotype and haplotype data in the ped format?

Hi everybody In the ped format for genotype, alleles of any SNP are represented by two columns (one for each allele, separated by a space). Is a column sufficient for the haplotype to...

27 February 2021 1,965 1 View