Hi All,
Ok, here is a follow up to what I posted earlier... It appears that the
problem is with ntt=3 rather than igb as I thought earlier. So I guess it
must be some problem with the random number seed used when restarting a
langevin dynamics temperature run.
I have now run a GC-CG DNA base pair dimer, the fact that this is not a
stable simulation is not an issue here, I can reproduce this with other
systems, using the following 4 option sets with the following common
options:
&cntrl
irest = XXX, ntx = XXX,
imin = 0, ntb = 0,
igb = XXX, ntpr = 1, ntwx = 0,
ntt = XXX, gamma_ln=1,
tempi = 0.0, temp0 = 300.0
nstlim = XXX, dt = 0.001,
cut = 999.,
/
Where irest=0 and ntx=1 for the cold starts and irest=1 and ntx=5 for the
hot start.
nstlim = 20 for run 1
Nstlim = 10 for run 2 (two lots of 10, first from the inpcrd and 2nd with
irest=1 from the restrt of the first run).
1) ntt=1, igb=0 - Works, gives same answer at end of both runs with only
minor roundoff error.
---------------
NSTEP = 20 TIME(PS) = 0.020 TEMP(K) = 2068.34 PRESS =
0.0
Etot = 368.9722 EKtot = 752.1632 EPtot =
-383.1910
BOND = 114.4514 ANGLE = 111.7397 DIHED =
64.8835
1-4 NB = 36.1320 1-4 EEL = -791.5054 VDWAALS =
-14.8855
EELEC = 95.9933 EHBOND = 0.0000 RESTRAINT =
0.0000
NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 2068.34 PRESS =
0.0
Etot = 368.9723 EKtot = 752.1633 EPtot =
-383.1910
BOND = 114.4514 ANGLE = 111.7397 DIHED =
64.8835
1-4 NB = 36.1320 1-4 EEL = -791.5054 VDWAALS =
-14.8855
EELEC = 95.9933 EHBOND = 0.0000 RESTRAINT =
0.0000
2) ntt=3, igb=0 - Gives different final answers because the restart job
has
a different kinetic energy.
---------------
NSTEP = 11 TIME(PS) = 0.011 TEMP(K) = 1576.22 PRESS =
0.0
Etot = 390.0206 EKtot = 573.2024 EPtot =
-183.1818
BOND = 335.0041 ANGLE = 65.7769 DIHED =
69.2148
1-4 NB = 37.6554 1-4 EEL = -773.6727 VDWAALS =
-13.7223
EELEC = 96.5621 EHBOND = 0.0000 RESTRAINT =
0.0000
NSTEP = 1 TIME(PS) = 0.011 TEMP(K) = 1579.47 PRESS =
0.0
Etot = 391.2023 EKtot = 574.3841 EPtot =
-183.1818
BOND = 335.0040 ANGLE = 65.7769 DIHED =
69.2148
1-4 NB = 37.6554 1-4 EEL = -773.6727 VDWAALS =
-13.7223
EELEC = 96.5621 EHBOND = 0.0000 RESTRAINT =
0.0000
NSTEP = 20 TIME(PS) = 0.020 TEMP(K) = 2046.35 PRESS =
0.0
Etot = 360.5249 EKtot = 744.1685 EPtot =
-383.6436
BOND = 112.9835 ANGLE = 112.4017 DIHED =
65.2995
1-4 NB = 35.9892 1-4 EEL = -791.5224 VDWAALS =
-15.0036
EELEC = 96.2084 EHBOND = 0.0000 RESTRAINT =
0.0000
NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 2045.13 PRESS =
0.0
Etot = 358.4004 EKtot = 743.7257 EPtot =
-385.3253
BOND = 111.8146 ANGLE = 111.0979 DIHED =
65.1386
1-4 NB = 35.8125 1-4 EEL = -790.9753 VDWAALS =
-14.6337
EELEC = 96.4201 EHBOND = 0.0000 RESTRAINT =
0.0000
3) ntt=1, igb=1 - Works, gives same answer at end of both runs with only
minor roundoff error.
---------------
NSTEP = 20 TIME(PS) = 0.020 TEMP(K) = 1799.79 PRESS =
0.0
Etot = 109.4745 EKtot = 654.5028 EPtot =
-545.0283
BOND = 197.4270 ANGLE = 105.5909 DIHED =
62.4461
1-4 NB = 35.0079 1-4 EEL = -789.2670 VDWAALS =
-16.2016
EELEC = 99.7123 EGB = -239.7438 RESTRAINT =
0.0000
NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 1799.79 PRESS =
0.0
Etot = 109.4744 EKtot = 654.5028 EPtot =
-545.0283
BOND = 197.4270 ANGLE = 105.5909 DIHED =
62.4461
1-4 NB = 35.0079 1-4 EEL = -789.2670 VDWAALS =
-16.2016
EELEC = 99.7123 EGB = -239.7438 RESTRAINT =
0.0000
4) ntt=3, igb=1 - Fails to get the same answer because the initial kinetic
energy is different.
---------------
NSTEP = 11 TIME(PS) = 0.011 TEMP(K) = 1378.75 PRESS =
0.0
Etot = 127.7082 EKtot = 501.3924 EPtot =
-373.6843
BOND = 394.3374 ANGLE = 65.6750 DIHED =
68.7875
1-4 NB = 37.4169 1-4 EEL = -772.6624 VDWAALS =
-15.0346
EELEC = 98.6876 EGB = -250.8917 RESTRAINT =
0.0000
NSTEP = 1 TIME(PS) = 0.011 TEMP(K) = 1381.78 PRESS =
0.0
Etot = 128.8073 EKtot = 502.4915 EPtot =
-373.6843
BOND = 394.3374 ANGLE = 65.6750 DIHED =
68.7875
1-4 NB = 37.4169 1-4 EEL = -772.6624 VDWAALS =
-15.0347
EELEC = 98.6876 EGB = -250.8917 RESTRAINT =
0.0000
NSTEP = 20 TIME(PS) = 0.020 TEMP(K) = 1782.29 PRESS =
0.0
Etot = 101.7170 EKtot = 648.1397 EPtot =
-546.4227
BOND = 194.6616 ANGLE = 106.5368 DIHED =
63.0522
1-4 NB = 34.8711 1-4 EEL = -789.3727 VDWAALS =
-16.2924
EELEC = 99.9635 EGB = -239.8427 RESTRAINT =
0.0000
NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 1780.68 PRESS =
0.0
Etot = 99.6503 EKtot = 647.5550 EPtot =
-547.9047
BOND = 193.6238 ANGLE = 105.4144 DIHED =
62.9620
1-4 NB = 34.7114 1-4 EEL = -788.7622 VDWAALS =
-15.9607
EELEC = 100.0955 EGB = -239.9889 RESTRAINT =
0.0000
All the best
Ross
/\
\/
|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk/ | PGP Key available on request |
Received on Wed Apr 05 2006 - 23:49:59 PDT
