bazinga
Hello NAMD users
My name is Babban and I have just started to use NAMD and I had been using CHARMM for a long time before that.
I have following queries regarding an MD simulation that I want to set up ?
1. I want to do a MD in Periodic Boundary Condition for my peptide which is like 350 amino acids in a combined Ethanol+Water System where Ethanol would be 40%
Can somebody explain me in good detail about doing that ?
2. Is there way one change/set pH in NAMD ?. I did not find such a thing in the tutorials?
3. At a pH of 7.4 ,my peptide will have some charge and I would need to put equivalent charge in my PDB unit cell to neutralize the system?. Those charges are to be put in local minima.
How do I achieve that?
Please advise.
In anticipation of an encouraging reply
Best regards
Babban
UBC
My name is Babban and I have just started to use NAMD and I had been using CHARMM for a long time before that.
I have following queries regarding an MD simulation that I want to set up ?
1. I want to do a MD in Periodic Boundary Condition for my peptide which is like 350 amino acids in a combined Ethanol+Water System where Ethanol would be 40%
Can somebody explain me in good detail about doing that ?
2. Is there way one change/set pH in NAMD ?. I did not find such a thing in the tutorials?
3. At a pH of 7.4 ,my peptide will have some charge and I would need to put equivalent charge in my PDB unit cell to neutralize the system?. Those charges are to be put in local minima.
How do I achieve that?
Please advise.
In anticipation of an encouraging reply
Best regards
Babban
UBC