AMBER Archive (2003)

Subject: AMBER: TEMP is not reaching 300K

From: sd233_at_georgetown.edu
Date: Thu Jul 24 2003 - 12:06:49 CDT

Dear AMBER USERS:

I am trying to do dynamics on protein in an explicit water molecules at
constant pressure,with Waterbox size is 16A.

Also I gave the option to control the TEMP. i.e. not to allow it go
beyond 300K.

With this I have two problems

1. TEMP increase is sudden and its reaching beyond 300K.

My INPUT is like below:

__________________________________________________________

     imin = 0, nmropt = 1,

     ntx = 1, irest = 0, lastrst=6000000, ntrx
= 1,

     ntxo = 1, ntpr = 1, ntrx = 1, ntwr
= 500,
     iwrap = 0, ntwx = 100, ntwv = 0, ntwe
= 1,
     ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0,

     temp0 = 300.0, tempi = 0.0, heat = 0.0, ig = 71277, dtemp =
5.0, tautp = 2.0,
     ntt = 1, ntf = 2, ntb = 2, igb =
0, nsnb = 5,
     ipol = 0, gbsa = 0,
     dielc = 1.00000, cut = 9.00000, intdiel = 1.00000,
     scnb = 2.00000, scee = 1.20000,

     ibelly = 0, ntr = 0,

     nstlim = 10000, nscm = 1000, nrespa = 1,
     t = 0.00000, dt = 0.00100, vlimit = 20.00000,

     ntp = 1, plevel = 1,
     pres0 = 1.00000, comp = 44.60000, taup = 0.20000,

     ntc = 2, jfastw = 0,
     tol = 0.00005,
 &end
 &wt type='TEMP0', istep1=0, istep2=6000,
                   value1=0.0, value2=300.0, &end
 &wt type='TEMP0', istep1=6001, istep2=10000,
                   value1=300.0, value2=300.0, &end
 &wt type='END' &end

__________________________________________________________________

Could anyone will help me out,

Thanks
Sincerely,
Sivanesan.D.

D.Sivanesan, Ph.D.
Dept. of Oncology,
Lombardi Cancer Center,
Georgetown University, DC 20057

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu