Hi~ I'm a graduate student studying MD simulation.
When they use SMD simulation, many researchers used the option: harmonic restraint.
Why do they use the option?
What does it mean?
Harmonic restraints can be used to enforce the distance between two atoms. This might be done, for example, with pseudo-bonds between a metal atom or ion and one or more ligands associated with the metal, but restraints could be imposed on any two atoms in order to maintain a certain distance.
I have restraint ZN atoms and equilibrated the system for the step equal to 20ns. Now what is the best option. Should I remove all the restraint at once or I need to remove the restraint gradually in production.
Please guide me how to gradually remove the restraint, if it is necessary?
I am using NAMD. regards,
Whether you impose such constraints at all, impose them gradually, release them gradually, or keep them in place depends on the research question(s) you are asking. Take a look at some examples published in the scientific literature for additional guidance on this points. One such example is in a paper by R. Shen et al. (2015). Article Structural Refinement of Proteins by Restrained Molecular Dy...
Thank You sir, I have tried removing all the restraints and run another 20 ns and the system looks fine. Both the Zinc atoms are in their proper location. Just want to know, how to apply gradual decrease to the restraint. I searched some documents, but all of them are explaining the procedure of restraining.
Please see the NAMD documentation on harmonic constraints/restraints:
http://www.ks.uiuc.edu/Research/namd/2.9/ug/node27.html
"ConstraintScaling < scaling factor for harmonic constraint energy function > Acceptable Values: positive Default Value: 1.0 Description: The harmonic constraint energy function is multiplied by this parameter, making it possible to gradually turn off constraints during equilibration. This parameter is used only if constraints is set to on."
Hi, I have a question on a similar topic, restraints in namd. Can someone tell me what is the difference between conskfile and conskcol ? ( I see the web of namd, but I could not understand the difference) . I review some tutorials and it seems they use both of them at the same time.
Thank you,
Basilio.
The difference is substantial.
Since conskfile is the name of file where constraints are set, conskcol describes the column in which restrained atoms are marked, so: in conskfile you point the name of your PDB file (so it's simply a filename), and in conskcol you tell NAMD in which column constrained atoms are marked (occupancy, beta etc.).
I see... , thank you a lot! One more question please, I hope you do not mind =) Now I understand the difference between conskfile and conskcol, but I still do not understand well the difference between conskfile and consref. I understand that that both of them are the same file. However, conskfile tell the applied force to the constraint, but the consref use the x,y,z coordinate, of the same file, as the " the reference positions for harmonic constraints" is that right? If so, what will be the difference that I saw, in an constraint atom , when I apply 1pN respect to other where I apply 500pN. Also, if conskfile define the force, then I do not care about any constant of force? I saw that in other software you define the constant of force instead of force (I know you can get the constant from the force, but I wonder just in case). THANK YOU A LOT!
Basilio.
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