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
&cntrl
imin=0,
ntc=2, ntf=2,
cut=12.0, igb=2, saltcon=0.2, gbsa=1,
intdiel=1.0, extdiel=78.5,
ntpr=50,
nstlim = 5000, dt=0.002,
ntt=1, tempi=0.0, temp0=300.0, tautp=1.0,
ntx=1, irest=0, ntb=0,
nscm = 1000,
ntr=1
/
keep all atoms restrained
1.0
RES 1 9
END
END
I have also done the equillibration ,
i have a doubt regarding this , why we are giving a restrain to the molecule
and
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
&cntrl
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,
/
eof
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 .
regards
maya
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Received on Wed Mar 31 2010 - 09:00:05 PDT
