AMBER Archive (2009)

Subject: [AMBER] Problem with REMD

From: parul sharma (sharmaparul7373_at_gmail.com)
Date: Thu Mar 12 2009 - 02:45:09 CDT

Dear All,

I am trying to run REMD simulation on a dipeptide (6 replicas) using the
input for one of the replica:

&cntrl
  imin=0,
  ntc=2, ntf=2,
  cut=99, igb=5, saltcon=0.2, gbsa=1,
  ntpr=50, surften=0.005,
  nstlim=1000, dt=0.002, numexchg=1000,
  ntt=3, gamma_ln=1, temp0=586,
  ntx=5, irest=1, ntb=0,
  ntpr=500, ntwx=500, ntwr=500, ntwe=500, nscm=1000,
&end
The groupfile used looks like:

#
# replica
#
-A -i boxeq240.in -p di.prmtop -o boxeq240.out -c crd240-1to1000ps -r
240.rst -x crd240
-A -i boxeq300.in -p di.prmtop -o boxeq300.out -c crd300-1to1000ps -r
300.rst -x crd300
-A -i boxeq375.in -p di.prmtop -o boxeq375.out -c crd375-1to1000ps -r
375.rst -x crd375
-A -i boxeq469.in -p di.prmtop -o boxeq469.out -c crd469-1to1000ps -r
469.rst -x crd469
-A -i boxeq586.in -p di.prmtop -o boxeq586.out -c crd586-1to1000ps -r
586.rst -x crd586
-A -i boxeq732.in -p di.prmtop -o boxeq732.out -c crd732-1to1000ps -r
732.rst -x crd732

However, i am not able to find rem.log as the output, also the boxeq240.out
is not showing any progress in the Atomic coordinates and velocities, and
looks like below:

   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
NGLY
General flags:
     imin = 0, nmropt = 0
Replica exchange
     numexchg= 1000
Nature and format of input:
     ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
     ntxo = 1, ntpr = 500, ntrx = 1, ntwr =
500
     iwrap = 0, ntwx = 500, ntwv = 0, ntwe =
500
     ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
     ntf = 2, ntb = 0, igb = 5, nsnb =
25
     ipol = 0, gbsa = 1, iesp = 0
     dielc = 1.00000, cut = 99.00000, intdiel = 1.00000
     saltcon = 0.20000, offset = 0.09000, gbalpha= 1.00000
     gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00500
     rdt = 0.00000, rgbmax = 25.00000
     alpb = 0
     scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
     ibelly = 0, ntr = 0
Molecular dynamics:
     nstlim = 1000, nscm = 1000, nrespa = 1
     t = 0.00000, dt = 0.00200, vlimit = 20.00000
Langevin dynamics temperature regulation:
     ig = 71277
     temp0 = 240.00000, tempi = 0.00000, gamma_ln= 1.00000
SHAKE:
     ntc = 2, jfastw = 0
     tol = 0.00001
| INFO: Old style inpcrd file read

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

Please help me to sort out this problem.

Thanks in Advance

regards
Parul Sharma 

-- 
With Best Regards

Parul Sharma
PhD Student, Durban University of Technology,
Durban,
South Africa
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