In order to do MD Simulation using NAMD software and CHARMM FF, I have used implicit water model and diel=4 but since my molecule is charged (DNA), I would like to know if I can use explicitions or should I just carry on with the simulation without charge-neutralizing ?
In implicit models the periodic boundary conditions are not employed, so you do not need to add charges to neutralize the system. But, you may include an ionic strength for ions in the solvent treated implicitly.
Thank you Hiqmet. I have used PME no and and dielectric 4 keywords in NAMD input conf file for simulation by implicit model. Is there any other wat to incorporate ionic strength in the input?
The keyword is: ionconcentration
It is given in molar, there is also a manual online for namd.
I tried to find details on "ionconcentration" keyword in NAMD. I have used dielectric=4.00 (implicit solvent). I want to use implicit model for water solvent. Im not sure what should be the value of dielectric. Also, where to give the keyword ionconcentratrion (as my system is DNA and is charged).
This has to go into the configuration NAMD file; the one that you use to specify other parameters such as dielectric constant. You should also have a look at the following link:
http://www.ks.uiuc.edu/Research/namd/2.9/ug/node31.html
I am having problem running NAMD using GBIS "on", the jobs gets terminated showing error message that it cannot detect keyword GBIS and so on. I thought of using both ionconcentration and dielectric keywords without GBIS. In that case the run gets terminated showing error that it cannot detect "ionConcentration" keyword. I guess using only dielectric and no PME is sufficient.
You should check your script. I just did some tests on my systems, using the following choices and it worked.
GBIS on
solventDielectric 80.0
ionConcentration 0.154
Running without GBIS as``on" state and without PME, you are doing dynamics in vacuum, which is not the same thing as implicit solvent dynamics.
Thank you Hiqmet. Its working with NAMD 2.9 but earlier I tried with NAMD 2.6 and it wasnt working. I have used charmm type parameters for the simulation. I have used CHARMM27 ff but it seems the ff does not take into account GBIS, so should I use some other ff? Also Im doin the simulation for nucleic acids, so should I do anymore changes?
Actually I tested on (top)par_all27_prot_na.* and (top)par_all27_prot_lipid.* in protein-peptide complex system and it works. I am using NAMD 2.8.
This discussion is helpful for me in gaining some points for my project..
since,i am new to this field,i was trying to simulate protein in implicit solvent,but i am struck with what are the initial procedure to follow,can i know the exact procedure to follow for implicit solvent simulation for protein..?
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