Rmsd analysis in Gromacs?

More Urszula Sylwia Uciechowska-Kaczmarzyk's questions See All

What methods are used to destroy digital data?

Hello everyone:) Can anyone recommend me some publications on data destruction? I am looking for e.g. publications concerning: - the use of microwave radiation in the destruction of data or data...

03 May 2023 4,612 5 View

Equlibration errors in GROMACS input file?

I am trying to run equilibration i gromacs 5.0.7 Implicit solvent. My input file is: ; MD CONTROL OPTIONS integrator = md dt = 0.002 nsteps =...

11 December 2017 6,826 0 View

Does anyone know a software/application that can be used for preparing a pictures of sequence alignment?

I am looking for a software for preparing nice (publication) pictures of sequence alignment.

02 March 2016 9,347 8 View

Any advice on single strand DNA in hairpin conformation?

Does anyone know how to build a ssDNA in hairpin conformation? Does anyone know maybe other software where I could do this? Thank you in advance for any suggestions.

01 February 2015 8,480 6 View

How do I prepapre DNA for NAMD simulations?

Is there any fast way to change the DC on CYT for NAMD?

22 January 2015 5,674 2 View

Why do I get this error while running psfgen for NAMD?

I want to run dsDNA-protein MD simulations. I have tried to use top_all36_na.rtf Iprepared a script to run psfgen: package require psfgenresetpsf topology charmm36.nbfix/top_all36_na.rtftopology...

31 December 2014 475 9 View

How do I prepapre DNA for NAMD simulations?

Is there any fast way to change the DC on CYT for NAMD?

31 December 2014 1,504 2 View

How can I determine the Hbond occupancy with GROMACS?

Dear Gromacs users, I would like to run H-bond analysis in order to get a percentage H-bond occupancy between protein and DNA. How can I do it? I used the g_bond command but the obtained plot does...

29 October 2014 5,918 13 View

With regards to Gromacs Radius of gyration, how do I analyse the data?

Does anyone know how to analyse the plot obtained from gyration? I know what it means but I'm not sure how to use this measure or interpret data? I run MD for a protein in complex with DNA.

21 October 2014 9,326 1 View

Is it possible to run RMSD calculations in GROMACS?

Is it possible to run RMSD calculations for the part of the protein for example rmsd for AA 45-187? How to specify it using g_rms command?

15 October 2014 1,220 5 View

Gromacs first step of minimization ?

I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...

07 August 2024 2,598 1 View

How to restart MD without using checkpint file in GROMACS?

Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar

29 July 2024 3,084 8 View

How to prepare a molecule for molecular dynamics calculations?

If I want to calculate molecular dynamics (Gromacs), do I first need to optimize the geometry of the molecule? For example, I first draw the molecule in Avogadro, and then what? I guess I can't...

28 July 2024 673 3 View

Wrong out put for gmx x2top?

Dear users, I would like to simulate a zeolite structure in gromacs. I got the .cif file from IZA expanded in one direction in Materials Studio and exported a .pdb file. However, when I want to...

24 July 2024 367 4 View

Why binding energy is in positive number after performing mmpbsa?

I performed mmpbsa of protein-protein complex simulation on gromacs. My binding free energy is +166781. This complex is stable when experimentally produced in wet lab. In index.ndx I grouped...

19 July 2024 4,120 5 View

How to resolve ‘[ atomtypes ] Invalid order for directive atomtypes’ error in Gromacs?

I have been using Gromacs 2021.7. I wanted to simulate two small molecules in water. But, while generating the ions.tpr, I am getting the following error. The topol.top and .itp files for each...

17 July 2024 9,897 4 View

Getting this error : gmx_mpi': corrupted size vs. prev_size: 0x0000000001d1b320 ***?

i am using the trjconv command in gromacs gmx_mpi -debug trjconv -s md.gro -f md.xtc -o utr.xtc -fit rot+trans and after few steps i got the error gmx_mpi': corrupted size vs. prev_size:...

17 July 2024 6,216 1 View

Can we find the Gromacs version from XTC file or TRR?

Hello everyone, This soudns like a strange question, but I created five XTC files using five different versions of GROMACS some years ago. All other files are missing, and I want to repeat the...

16 July 2024 7,205 2 View

How to define a zeolite structure with rigid framwork?

Dear Gromacs users, I would like to simulate a zeolite-water system. In different literature, it is suggested to consider a rigid framework of zeolite to decrease the computational cost. I would...

15 July 2024 4,590 1 View

In silico techniques for identification of inhibitor/activator/substrate activity?

Hello dear researchers, I would like to know about available in silico tests that could predict the activity of ligands (small molecules) against the target protein. I have performed docking...

08 July 2024 4,724 4 View