AMBER Archive (2006)

Subject: AMBER: negative T_solv values

From: Markus O Kaukonen (mokaukon_at_cc.helsinki.fi)
Date: Wed Feb 15 2006 - 02:25:40 CST

Dear all,

I'm running Amber 8 on i686 linux, protein solvated in water, with
truncated octahedral box. A set of atoms are restrained

When doing MD with constant pressure Berendsen I get negative
T_solv in the energy output (T_solute is OK)
Is there a reason to worry??????????

grep 'L1' mden3
L1 Temp T_solute T_solv Pres_scal_solu
L1 0.3040831341E+03 0.3040831341E+03 -.6227231148E+11 0.1000000000E+01
L1 0.3057773067E+03 0.3057773067E+03 -.6311871115E+11 0.1000000000E+01
L1 0.3014033680E+03 0.3014033680E+03 -.6382077598E+11 0.1000000000E+01
L1 0.3042764873E+03 0.3042764873E+03 -.6433882271E+11 0.1000000000E+01
L1 0.3046080073E+03 0.3046080073E+03 -.6472413109E+11 0.1000000000E+01
L1 0.3011210309E+03 0.3011210309E+03 -.6493511085E+11 0.1000000000E+01
........................................................................

My input is :
Hydrog,medQM,Unoohip,GLH8,50 ps QM restrained, const p, allH free(but
shake)
  &cntrl
    irest=1,ntx=5, !velocities read
    nstlim=25000,dt=0.002, !25000 steps 2 fs dt
    temp0=300.0,ntt=1,tautp=1.0, !ref temp, Berendsen,temp time const
    ntc=2,ntf=2, !shake bonds with hydrogen are
constrained
    cut=8.0, !cutoff for non-bonded
    ntpr=1000,ntwx=1000,ntwv=0,ntwe=1000, !print interwalls
    ntb=2,ntp=1,pres0=1.0,taup=1.0,!const p, isotropic, ref.p1bar,Prelax
time
    ipol=0,igb=0, !no polaricity, no Born
    scnb=2.0,scee=1.2, !1-4vdW factor,1-4ee factor
    ibelly=0, !NO frozen atoms
    ntr=1,restraint_wt=100, !restrained atoms, harmonic force
   &end
List of restrained atoms (QM, no H)
GRP1
ATOM 2559 2559
ATOM 2562 2562
....etc.......

........................................................................

Terveisin Markus

-----------www= http://www.iki.fi/markus.kaukonen---------------
Markus.Kaukonen_at_teokem.lu.se \ HOME-> Viinirinne 3 F 12
Dep. of Theoretical Chemistry \_______ 02630 Espoo, Finland
Lund University \ tel:+358-(0)9-5127122/h
Chemical Centre, P. O. Box 124 \____
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