I am interested in this technique. Beyond the methodological background can you suggest any reference where accelerated MD has been performed with the GROMACS package? In my lab we do not have AMBER yet.
i thin most of the steered molecular dynamics is done with NAMD
How can I convert a trajectory file from GROMACS (trr or xtc format) to AMBER (ASCII or NetCDF format)? I have always seen tutorial about the revers procedure, ie from AMBER to GROMACS...
06 July 2014 2,240 4 View
From what I have understood (from the AMBER manual) I have to prepare the topology of every single mutant I want to scan and, subsequently, I have to start an individual run (with the MMPBSA.py...
05 June 2014 3,637 1 View
I am looking for a forcefield in GROMACS which better characterizes the TCDD ligand. In particular I have found that OPLS-AAx seems suitable [J Chem Theory Comput. 2012 Oct...
01 February 2014 5,031 4 View
Since I have MDs produced with GROMACS, are there available any tool for calculating dGs with MM/GBSA method? (and, in the meanwhile, without converting trajectories in AMBER format?)
01 February 2014 7,279 9 View
Does anyone have a "reference manual" of such forcefield? (especially the related top files in GROMACS) e.g. what are the atom types included and what they describe, etc. etc.
31 December 2013 5,649 3 View
I need to create a topology file (.top for GROMACS) of 2,3,7,8-TCDD (dioxin). In particular my topology file will have to be suited for implementing OPLS-AA forcefield, since I know that the...
31 December 2013 2,096 9 View
I have to accomplish an homology modeling task in which the reference template does not cover very large loops of the query sequence (20-30 residues). I have not found any reliable alternative...
11 December 2013 8,518 3 View
...ma 'sto paper quando uscirà???
01 January 1970 1,143 0 View
Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...
06 August 2024 1,495 2 View
kindly reply me. Thanking you in advance.
05 August 2024 7,727 4 View
Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...
03 August 2024 3,371 3 View
I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?
02 August 2024 3,143 4 View
Molecular docking software/ websites?
02 August 2024 8,704 7 View
Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out? For example consider a process for certain product manufacture where a new process flow...
31 July 2024 781 1 View
Dear all, I am working on particle deposition in human's & rat's respiratory airways using CFD and I am looking for the 3D CAD file for my simulations (STEP or IGES format). If somone has such...
29 July 2024 1,092 2 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
Good day, I am a student trying to work on Autodock for a project regarding Ligand-DNA interaction so i am quite new to molecular docking. i have followed tutorials and did all the steps...
28 July 2024 2,136 4 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