Can anyone explain the difference between these three advanced molecular dynamic techniques?
My protein is 476 residues. I would like to plot the map only for specific regions and mention it in the input thus choosing the residues i wish to calculate the contacts for. Does anyone know of...
10 November 2014 6,542 9 View
Can the changes in radius of gyration of elongated protein also tell the compactness of the protein? If yes, is a difference in Rg of 30 A significant? Thanks in advance.
09 October 2014 7,109 6 View
I have performed the principal component analysis in gromacs and I have obtained the projection of eigen vectors PC1 vs PC2 plot as in figure 4BI would like to add information about the...
08 September 2014 4,909 5 View
What could be the molecular basis for the protein to twist and undergo a conformational change intrinsically (that does not involve any substrate binding event) ?
08 September 2014 5,904 2 View
I would like to plot no. of water molecules within a cut-off distance as a function of time. Any gromacs utility that will help me? Thanks in adv
08 September 2014 5,350 5 View
Any gromacs utility to measure radius of curvature? How is it different from the radius of gyration?
07 August 2014 3,818 2 View
I would like to get the names of a few proteins that show bending dynamics in solution. Are there any transport proteins that shown similar movements? Kindly post them here. Thanks in advance.
05 June 2014 6,829 8 View
I have simulated an elongated protein in a cubic box (reason being the long edges of the protein tilt during simulation and interact with its periodic image thus resulting in bad energy values...
05 June 2014 8,027 5 View
In two domain proteins there are movements possible along the hinge. Is anyone aware of the energy involved in this hinge movement?
05 June 2014 10,032 9 View
How do I specify this in the mask for AMBER ptraj? Protein residues are from 1-400. But I want to leave out two loop regions,100-105 and 250-255. The RMSD plot fluctuates and I presume leaving out...
03 April 2014 767 28 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
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
I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the...
04 August 2024 1,200 2 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