[AMBER] water simulation

From: subrata paul <paul.subrata34.gmail.com>
Date: Mon, 10 Jan 2011 18:21:38 +0400

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
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