NAMD Wiki: NamdQuestions

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Q: I am trying to add a surface molecule to a nanopore. Any suggestions on how to go about doing this? Thanks!


Common or unresolved questions about NAMD and NAMD use.


Q: I wonder to know how I can define a new force field in NAMD, preferably using C++? I also want the code to be run on GPUs? Thanks, -Kasra Momeni


I wonder if NAMD can simulate the binding procedure of a ligand on a protein and the conformational changes of the ligand in this process. Thanks


I'm interested in modeling the folding of a small protein attached at one end to a flat plane (in reality the exterior of a cell membrane). Is there a way to impose that plane as a boundary condition, and to fix the coordinates of one amino acid to always be attached to the plane?

-BeckettSterner


Suppose I am doing simulation with three molecules together. At the end of a certain simulation say i want to find the intermolecular binding energies, how can do that by?

You can use the NAMD 2.5 pair interaction feature to estimate this. See the final example at http://www.ks.uiuc.edu/Research/namd/2.5/ug/node39.html and the parameters at http://www.ks.uiuc.edu/Research/namd/2.5/ug/node36.html -JimPhillips


Does NAMD do TMD?

The latest version of CHARMM has a very interesting "zeta form" of targeted molecular dynamics:

http://biobos.nih.gov/apps/charmm/charmmdoc/c32a1/tmd.html

Is there anything similar in NAMD?

My understanding is that steered MD is not the same as targeted MD. I would like to be able to do TMD with NAMD.

Thanks!

Paul

My understanding is that both are built in now, though I have not used them. Please see this documentation. http://biowulf.nih.gov/apps/namd/namd-ug/node33.html#SECTION00096500000000000000


Does NAMD create new bonds? For example, if I have a certain number of hydrogen bonds specified in my PSF initially and two atoms come close enough to form a new hydrogen bond, could NAMD simulate that? Or is it that the bonds specified in the PSF initially are the same ones at the end?


No new bonds can be added during a namd run, hydrogen bonds are special cases of electrostatic interactions. However, if you employ free energy perturbation methods small changes to bonds can be made, over many sets of small simulations. Brian


Energy Profiles.

Can I use NAMD to generate a energy profile for a given protein structure, using differents combinations of force fields implemented in NAMD ?
 

Q: Is there a document that provides an overview of the source code architecture, C++ classes, coding convention, etc.?

A: A quite old NAMD programming guide is here: http://www.ks.uiuc.edu/Research/namd/1.5/pg.ps

Q: Is there a more recent programming guide? I would like to develope a little Plugin.


Q: If I want to pull two atoms together (not tMD or sMD or constantForce) by placing a "bond" between them, how would I do that in NAMD?