dear sir,
I am simulating a system containing only water in amber 10
I made the system using following command..
1. xleap -s -f leaprc.GLYCAM_06
2. x=copy SPC
3. solvatebox x SPCBOX 12.0
4. saveamberparm x x.prmtop x.inpcrd
Is this correct way for making the system?????
Then i minimiz the system..my input is.
min.in
&cntrl
imin=1,maxcyc=2500, ncyc=1000, ntx=1, ntb=1,ntmin=2,
cut=10.0
/
After that
I run Npt simulation....
md.in
&cntrl
imin=0,ntt=1,tempi=300.0 ,temp0=300.0, dt=.001,
ntpr=500, ntwx=1000, ntwx=500,
ntb=2,ntp=1,pres0=1,
cut=10, vrand=1,
nstlim=100000
/
After MD simulation, I ploted RDF for OW_HW by ptraj
trajin xxxxx.mdcrd
radial OW_OH .1 10 :WAT.O :WAT.H*
after ploting in xmgrace I got a sharp peak of hight 25 at .98.
Is this peak for bonded Hydrogen atom ????
I have attached Rdf plot herewith.
Why this is happen ??????? am i worng in the above procedure????
please help me regarding this...
thanking u
subrata-
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Received on Mon Jan 10 2011 - 06:30:05 PST
