Sir
I have simulated 40-mer DNA using following NAB program.
molecule m;
m = fd_helix( "abdna", "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa", "dna" );
putpdb( "nuc20.pdb", m, "-wwpdb");
then using xleap "leaprc.ff99bsc0" I built prmtop and inpcrd files.
then I did minimization.
lastly I start heating using following step
Stage 1 heating of polyAT 0 to 50K
&cntrl
imin=0, irest=0, ntx=1,
nstlim=10000, dt=0.0005,
ntc=2, ntf=2,
ntt=1, tautp=1.0,
tempi=0.0, temp0=50.0,
ntpr=50, ntwx=50,
ntb=0, igb=0,
cut=12.
/
but when temperature arrise to 250K ,one strand of DNA is disappeared.
I want to my heating step is right or wrong.
Give me suggestions
--
SHESH NATH
RESEARCH SCHOLAR,
THEORETICAL CONDENSED MATTER PHYSICS,
DEPARTMENT OF PHYSICS,
BANARAS HINDU UNIVERSITY,
VARANASI-221005
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Received on Mon Jan 10 2011 - 20:30:04 PST
