Dear AMBER Users:
I have done a practice run with a dipeptide before going into deeper waters.
I took this sample run from the $OML_AMBER/test/sander directory, where I
have increased the nrun values.
These are my input files after minimizing the system...
=-=-=-=-=-=
(MD_1.IN)
# md using sander. Raise temp from 0->300 'slowly'.
&cntrl
irest=0, ntx=1, imin=0, nrun=10, nstlim=100,
nsnb=25, tempi=0.0, temp0=10.0, ntt=5,
ntc=2, ntf=2, idiel=1, cut=8.0, ntb=1, nmropt=1, iftres=0,
ntpr=10, scee=2.0, ntwe=10,
&end
#Raise the target temp. from 10->300 over the 1st 100 steps:
&wt type = 'TEMP0', istep1 = 0, istep2 = 100,
value1 = 10.0, value2 = 300.0, iinc = 5, &end
&wt type = 'END', &end
(MD_2.IN)
final warming with ewald
&cntrl
iewald = 1, idiel = 1, scee = 1.2,
cut = 9.0, nsnb = 10,
ntx = 7, irest = 1,
ntf = 2, ntc = 2, tol = 0.0005,
ntb = 2, ntp = 1,
nstlim = 100, nrun = 10,
ntpr = 10, ntwe = 10,
&end
25.685286 21.554192 19.621214 90.0 90.0 90.0
25 25 25 4 0 0 0
0.000001
=-=-=-=-=-=
However, after the jobs are done and after examining the output files,
neither the TEMP or the PRESS values indicate that they performed as
told; i.e. TEMP does not reach 300 K within 100 steps (MIN_1.IN) nor
PRESS is kept constant (MIN_2.IN).
Can anybody tell me what I am doing wrong?. I will appreciate any hint.
Much obliged,
Ramon
The following lines are a summary of the output files...
MIN_1.OUT
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.00
NSTEP = 10 TIME(PS) = 0.010 TEMP(K) = 20.64 PRESS = 0.00
NSTEP = 20 TIME(PS) = 0.020 TEMP(K) = 53.54 PRESS = 0.00
NSTEP = 30 TIME(PS) = 0.030 TEMP(K) = 73.20 PRESS = 0.00
NSTEP = 40 TIME(PS) = 0.040 TEMP(K) = 83.66 PRESS = 0.00
NSTEP = 50 TIME(PS) = 0.050 TEMP(K) = 93.89 PRESS = 0.00
NSTEP = 60 TIME(PS) = 0.060 TEMP(K) = 104.97 PRESS = 0.00
NSTEP = 70 TIME(PS) = 0.070 TEMP(K) = 114.69 PRESS = 0.00
NSTEP = 80 TIME(PS) = 0.080 TEMP(K) = 127.17 PRESS = 0.00
NSTEP = 90 TIME(PS) = 0.090 TEMP(K) = 144.96 PRESS = 0.00
NSTEP = 100 TIME(PS) = 0.100 TEMP(K) = 159.51 PRESS = 0.00
NSTEP = 100 TIME(PS) = 0.100 TEMP(K) = 93.09 PRESS = 0.00
NSTEP = 100 TIME(PS) = 0.100 TEMP(K) = 45.28 PRESS = 0.00
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
NSTEP = 1 TIME(PS) = 0.901 TEMP(K) = 50.26 PRESS = 0.00
NSTEP = 10 TIME(PS) = 0.910 TEMP(K) = 50.22 PRESS = 0.00
NSTEP = 20 TIME(PS) = 0.920 TEMP(K) = 50.17 PRESS = 0.00
NSTEP = 30 TIME(PS) = 0.930 TEMP(K) = 47.62 PRESS = 0.00
NSTEP = 40 TIME(PS) = 0.940 TEMP(K) = 48.21 PRESS = 0.00
NSTEP = 50 TIME(PS) = 0.950 TEMP(K) = 48.26 PRESS = 0.00
NSTEP = 60 TIME(PS) = 0.960 TEMP(K) = 47.32 PRESS = 0.00
NSTEP = 70 TIME(PS) = 0.970 TEMP(K) = 47.53 PRESS = 0.00
NSTEP = 80 TIME(PS) = 0.980 TEMP(K) = 47.16 PRESS = 0.00
NSTEP = 90 TIME(PS) = 0.990 TEMP(K) = 45.68 PRESS = 0.00
NSTEP = 100 TIME(PS) = 1.000 TEMP(K) = 44.47 PRESS = 0.00
NSTEP = 100 TIME(PS) = 1.000 TEMP(K) = 47.93 PRESS = 0.00
NSTEP = 100 TIME(PS) = 1.000 TEMP(K) = 1.59 PRESS = 0.00
MIN_2.OUT
IG = 71277 TEMPI = 0.00 HEAT = 0.000
NRUN = 10 NTT = 0 TEMP0 = 300.000
DTEMP = 0.000 TAUTP = 0.200 TAUTS = 0.200
NSTEP = 1 TIME(PS) = 1.001 TEMP(K) = 44.51 PRESS = -3145.28
NSTEP = 10 TIME(PS) = 1.010 TEMP(K) = 47.09 PRESS = -2650.07
NSTEP = 20 TIME(PS) = 1.020 TEMP(K) = 47.73 PRESS = -2162.29
NSTEP = 30 TIME(PS) = 1.030 TEMP(K) = 48.51 PRESS = -1804.37
NSTEP = 40 TIME(PS) = 1.040 TEMP(K) = 49.28 PRESS = -1604.27
NSTEP = 50 TIME(PS) = 1.050 TEMP(K) = 49.76 PRESS = -1496.84
NSTEP = 60 TIME(PS) = 1.060 TEMP(K) = 50.99 PRESS = -1423.33
NSTEP = 70 TIME(PS) = 1.070 TEMP(K) = 50.91 PRESS = -1331.93
NSTEP = 80 TIME(PS) = 1.080 TEMP(K) = 49.51 PRESS = -1257.14
NSTEP = 90 TIME(PS) = 1.090 TEMP(K) = 51.27 PRESS = -1204.47
NSTEP = 100 TIME(PS) = 1.100 TEMP(K) = 51.28 PRESS = -1077.26
NSTEP = 100 TIME(PS) = 1.100 TEMP(K) = 49.32 PRESS = -1692.42
NSTEP = 100 TIME(PS) = 1.100 TEMP(K) = 1.71 PRESS = 537.21
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
NSTEP = 1 TIME(PS) = 1.901 TEMP(K) = 80.74 PRESS = -208.99
NSTEP = 10 TIME(PS) = 1.910 TEMP(K) = 81.84 PRESS = -212.90
NSTEP = 20 TIME(PS) = 1.920 TEMP(K) = 81.35 PRESS = -200.40
NSTEP = 30 TIME(PS) = 1.930 TEMP(K) = 83.21 PRESS = -213.10
NSTEP = 40 TIME(PS) = 1.940 TEMP(K) = 81.04 PRESS = -157.10
NSTEP = 50 TIME(PS) = 1.950 TEMP(K) = 79.93 PRESS = -146.96
NSTEP = 60 TIME(PS) = 1.960 TEMP(K) = 78.70 PRESS = -151.27
NSTEP = 70 TIME(PS) = 1.970 TEMP(K) = 80.03 PRESS = -185.09
NSTEP = 80 TIME(PS) = 1.980 TEMP(K) = 80.12 PRESS = -126.99
NSTEP = 90 TIME(PS) = 1.990 TEMP(K) = 79.62 PRESS = -20.18
NSTEP = 100 TIME(PS) = 2.000 TEMP(K) = 80.31 PRESS = 53.78
NSTEP = 100 TIME(PS) = 2.000 TEMP(K) = 80.66 PRESS = -148.81
NSTEP = 100 TIME(PS) = 2.000 TEMP(K) = 1.22 PRESS = 71.87
--
"There are so many ways....
There is so little time...."
"Hay tantos caminos.....
Pero, hay tan poco tiempo....."
___________________________________________________________________________
Dr. Ramon Garduno-Juarez
Research Professor in Biophysics
CENTRO DE CIENCIAS FISICAS | EMAIL: ramon_at_ce.fis.unam.mx
UNIVERSIDAD NAL. AUTONOMA DE MEXICO |
Apdo. Postal 48-3 | VOICE: +52(5)6227749 ; +52(7)3291749
62251 Cuernavaca, Morelos |
MEXICO | FAX: +52(5)6227775 & +52(7)3291775
___________________________________EOF ____________________________________
Received on Mon Dec 04 2000 - 19:39:24 PST
