01 January 2016 0 3K Report

hello everyone,

I am using RexMD method for molecular simulations of a nucleic acid, using AMBER 14. I am following the AMBER TUTORIAL page where i have built the structure and started the equillibration dynamics but i am confused with the final production dynamics where tutorial suggested 1 ns run but i want to increase upto 50ns. can you please suggest the variable that i should change to achieve higher time scale?

this is the parameter file from AMBER website.

Equilibration

&cntrl

irest=0, ntx=1,

nstlim=500, dt=0.002,

irest=0, ntt=3, gamma_ln=1.0,

temp0=XXXXX, ig=RANDOM_NUMBER,

ntc=2, ntf=2, nscm=1000,

ntb=0, igb=5,

cut=999.0, rgbmax=999.0,

ntpr=100, ntwx=1000, ntwr=100000,

nmropt=1,

numexchg=1000,

/

&wt TYPE='END'

/

DISANG=ala10_chir.dat 

Similar questions and discussions