AMBER Archive (2004)

Subject: AMBER: umbrella sampling

From: tang kwa (nongtangkwa_at_yahoo.com)
Date: Thu Jul 29 2004 - 12:25:00 CDT

Dear all,

Now I am trying to calculate PMF using umbrella
sampling. I got the problem in the history file. It
showed the torsion angle is zero in all steps. Could
anyone please give me any idea to solve it?

this is my input:
 
test of umbrella sampling of a chi torsion angle
 &cntrl
   nstlim=100, cut=99.0, igb=1, saltcon=0.1,
   ntpr=1, ntwr=10, ntwx=10,ntt=3, gamma_ln=0.2,
   ntx=1, irest=0,ntc=2, ntf=2, tol=0.000001,
   dt=0.001, ntb=0, nmropt=1,

 &wt
   type='DUMPFREQ', istep1=10,
 &end
 &wt
   type='END',
 &end
DISANG=RST
DUMPAVE=chi_vs_t.0
LISTIN=POUT
LISTOUT=POUT

-----RST file -----------
# 1 MOL CHIr: (1 MOL O1)-(1 MOL C7)-(2 MOL O1)-(2 MOL
C7) 0.0 0.0
 &rst iat = 43, 21, 43, 21,
       r1 =-180.0, r2 = 0.0, r3 = 0.0, r4 = 180.0,
       rk2 = 30.0, rk3 = 30.0, &end
                  

---this is file 'chi_vs_t.0'----
       0 0.000
       0 0.000
      10 0.000
      20 0.000
      30 0.000
      40 0.000
      50 0.000
      60 0.000
      70 0.000
      80 0.000
      90 0.000
 
Thank you in advance!
TK

        
                
__________________________________
Do you Yahoo!?
New and Improved Yahoo! Mail - 100MB free storage!
http://promotions.yahoo.com/new_mail
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu