Dear Amber Users:
I am trying to do dynamics of a double crossover DNA molecules (there is
crossover between two double helix at specific location). There are 76
base
pairs. I have solvatd the systems and added Na+ ions. I could do
minimization hloding the DNA fixed (ntr=1). After 8000 minimzation steps
when I try to do NVT dynamics (still holding the DNA fixed) and gradually
try to increase the temp. to 300 (below is the ctl file), I get even after
11 ps too many warning for vlimit exceed. It seems the solute temparature
is too high in th erange of 10000k whereas solvent in the range 300K.
I tried the option ntt=5 with tautp = 0.2 and imgslt = 1, but it is the
same situation. I also tried with both nmropt=0/1, it is same situation.
When I tried to do NPT dynamics to get the correct water density (again
holding the DNA) it crash immediately saying many atoms excape.
Any suggestion will be of great help.
Prabal
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&cntrl
timlim = 999999., nmrmax = 1, nmropt=1,
ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
ntpr = 100, ntwx = 500, ntwv = 0, ntwe = 0,
ntwxm = 1, ntwvm = 999999, ntwem = 999999, ioutfm = 0,
ntwprt = 0,
ntf = 2, ntb = 1, idiel = 1, dielc = 1.0,
cut = 9.0, ntnb = 1, nsnb = 10, ntid = 0,
scnb = 2.0, scee = 1.2, cut2nd = 0.0, ichdna = 0,
isftrp = 0, rwell = 0.0,
ipol = 0,
ibelly = 0, ntr = 1,
imin = 0,
nrun = 1,
nstlim = 22500,
ndfmin = 0, ntcm = 0, nscm = 0,
init = 3, t = 0.0, dt = 0.001,
temp0 = 300.0, tempi = 100.0,
ig = 71277, heat = 0.0,
ntt = 5, isolvp = 0, dtemp = 0.0,
tautp = 0.2, tauts = 0.2,
vlimit = 15.0,
tauv0 = 0.0, tauv = 0.1, vzero = 0.0,
ntp = 0, pres0 = 1.0, comp = 44.6,
taup = 0.2, npscal = 1,
ntc = 2, tol = 0.00001,
imgslt = 1, iftres = 1,
jfastw = 0,
ivcap = 0, matcap = 0, fcap = 1.5,
&end
&wt
type='TEMP0', istep1=0, istep2=500,
value1=100.0, value2=300.0,
&end
&wt
type='TEMP0', istep1=500, istep2=12500,
value1=300.0, value2=300.0,
&end
&wt
type='END',
&end
&rst
iat=0,
&end
Hold the DNA fixed
500.0
RES 1 153
END
END
--
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Prabal K Maiti Email:maiti_at_wag.caltech.edu
Beckman Institute (139-74) pkmaiti_at_yahoo.com
California Institute of Technology Tel:626-395-8151 (O)
400 South Wilson Avenue :626-744-1363 (H)
Pasadena, CA 91125 Fax:626-585-0918
Home add: 110 S. Michigan Ave.
http://www.wag.caltech.edu/home/maiti Apt # 19, Pasadena, CA 91106
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Received on Thu Feb 21 2002 - 19:23:39 PST
