I have done SMD of telomeric quadruplex DNA using NAMD software, GBIS implicit solvent model and CHARMM-27 ff. I have pulled the center of mass of the 1st base keeping center of mass of the last base fixed. I am very confused about the direction of pulling. I am attaching here the tcl script (which specifies force direction) I have used.
I don't understand why are you confused - in the SMD you choose your pulling direction "as you want" and it strongly depends on the system, so even if you provide your script it's almost impossible to us to qualify if it's wrong or ok :]
And - in addition - you don't need additional tcl scripts to perform SMD - everything is built in NAMD & it simply can be done by adding a couple of lines in "standard" input.
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