[AMBER] reg-Generalized Born Approach

From: maya maya <harish.maya83.gmail.com>
Date: Wed, 31 Mar 2010 21:21:33 +0530

Dear Amber !

i am tring to do Generalized Born Approach for DNA ,

In the tutorial file i saw the normal minimization procedure
and i gave the igb=2 , I have done the minimization ,
for equillibration i saw in earlier tutorial (
http://www2.umdnj.edu/~kerrigje ) script as follows

 equilibrate and heat structure
  ntc=2, ntf=2,
  cut=12.0, igb=2, saltcon=0.2, gbsa=1,
  intdiel=1.0, extdiel=78.5,
   nstlim = 5000, dt=0.002,
   ntt=1, tempi=0.0, temp0=300.0, tautp=1.0,
   ntx=1, irest=0, ntb=0,
   nscm = 1000,
  keep all atoms restrained
RES 1 9

I have also done the equillibration ,

i have a doubt regarding this , why we are giving a restrain to the molecule
i also i tried with out giving the restrain but the molecule (dna duplex -
the chains went apart)
why is it so and how come one can take such a restrained structure to do
dynamics ?

2) my second doubt is ,
in the mdrun also they have given the script as

 run MD at 300K
  ntc=2, ntf=2,
  cut=12.0, igb=2, saltcon=0.2, gbsa=1,
  intdiel=1.0, extdiel=78.5,
  ntpr=50, ntwx=50,
  nstlim = 25000, dt=0.002,
   ntt=1, tempi=300.0, temp0=300.0, tautp=2.0,
   ntx=1, irest=0, ntb=0,
   nscm = 1000,

 why they have given the ntx= 1 and the irest=0

if it is right if one wants to restart the same run, what will be the
values given to the same .

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Received on Wed Mar 31 2010 - 09:00:05 PDT
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