dear amber ,
I am doing TMD using amber ,
I have took two structures
and minimized them and equillibriated them
separately and with that ,
I have fixed one as the reference structure and the other as a Target ,
I have started doing TMD in vaccum .
The two structures are having same number of atoms ,
and they have a rmsd difference greaterthan 10 .
as if now I am making the input file ,
my input file is as follows
&cntrl
imin = 0,
irest = 0 ,
ntb = 0,
ntxo = 1,
ntx =1,
tempi =300.0
ntb = 0,
ntc=2,
ntf = 2,
igb = 1,
nscm = 100,
ntwr = 1000
ntpr = 100,
ntwx = 100,
ntwv =100,
ntwe = 100,
ntt = 3,
gamma_ln = 1.0,
temp0 = 300.0
nstlim = 10000000,
dt = 0.001,
cut = 12.0,
itgtmd=1,
tgtrmsd =15 ,
tgtmdfrc = 1.0
tgtfitmask= ":",
tgtrmsmask=":"
/
i didnot gave any mask , and i want to know wether i have given the TMD flags correct ,
the two flags are confusing ,
tgtrmsd
tgtmdfrc
in the way how we have to give values for it while doing the simulation based on the two structures of interest ,
and how one can give the force to the target molecule ,
thanks in advance !
balaji
UOM
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Received on Wed Feb 18 2009 - 01:25:58 PST
