Does anyone know if there is a tutorial for Computational Alanine Scanning using GROMACS?
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
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
I am looking for a software for preparing nice (publication) pictures of sequence alignment.
02 March 2016 9,347 8 View
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
Is there any fast way to change the DC on CYT for NAMD?
22 January 2015 5,674 2 View
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
31 December 2014 1,504 2 View
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
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 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
I have virus (viral hemorrhagic septicemia virus) in suspension and the experiment will not involve cells. What level of TCID50 is preferred?
11 August 2024 3,115 1 View
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
I am working on a SEM model where i have 7 latent variables (6 exogenous and 1 endogenous). In AMOS when I co-vary the exogenous constructs, only 2 paths are coming significant out of 6. But when...
03 August 2024 6,028 4 View
Suppose I am studying the construct of "Academic Motivation" (latent variable) in students, which is measured through three observed variables: "Intrinsic Motivation," "Extrinsic Motivation," and...
31 July 2024 3,913 6 View
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
Can a researcher use small sample size of 40 while using SEM with bootstrapping of 1000 and is it possible to get published
28 July 2024 4,402 2 View
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
Does it exist some special technique for cutting ceramic membranes for Cross-sectional FESEM or SEM images?
25 July 2024 5,482 2 View
I have an issue with SEM imaging of liposomes. When measured by DLS, they appear to be around 120 nm, but when using SEM with simple air drying, they appear much larger, around one micrometer.
25 July 2024 3,395 3 View
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