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.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 \____
S-221 00, Lund, Sweden \______ H+ ______
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Received on Sun Feb 19 2006 - 06:10:13 PST
