Dear Users !
i am beginner to amber
I am trying to do the targeted molecular dynamics from A to B DNA .
I have a doubt in my input files.
If i give the input files, as below , the convergence of the RMSD happens very fast but , i have read in papers
that the rmsd can be controlled in a linear way , could any one tell me how to use the flags for that .
my input file
duplex to A_B_DNA TMD with solvent PBC
&cntrl
imin = 0, ntx=5, nstlim=200000,
irest =1,
ntb = 2,
pres0 = 1.0,
nrespa=1,
ntp =1 ,
ntxo = 1,
tempi =300.0,
ntc=2,
ntf = 2,
nscm = 0,
ntwr = 1000
ntpr = 1000,
ntwx = 1000,
ntwe = 1000,
ntt = 3,
gamma_ln = 1.0,
temp0 = 300.0,
dt = 0.001,
scee=1.2,
cut =9.0,
itgtmd=1,
tgtrmsd =6.8 ,
tgtmdfrc =1,
tgtfitmask= ":1- 28"
tgtrmsmask= ":1- 28"
/
thanks in advance
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Received on Fri Mar 02 2012 - 12:00:02 PST
