Dear Amber-users,
When I ran MD (pmemd), I got an error like below (shown in 32ps point). My
system has ~83,000 atoms including water molecules. I did energy minimization
two times (with and without hoding solutes), and then heat up the system from 0
to 298K for 20ps. During those, there was no error and problem. But, when I
started MD of my system (starting at 20ps), I got an error like below.
I searched for this forum, and see that I can reduce timesteps or heat up my
system slowly. I think that I have reasonable timestep (2 fs) and I alredy
heated up the system slowly for 20ps.
Here, I attach energies of the system, and my md.in script. Could you tell me
how to handle this problem?
Thanks for your help in advance.
--------------------------------
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -362761.1854 EKtot = 0.0000 EPtot = -362761.1854
BOND = 97.2469 ANGLE = 456.8249 DIHED = 1219.9639
1-4 NB = 729.1620 1-4 EEL = -10159.2362 VDWAALS = 65513.4560
EELEC = -420618.6029 EHBOND = 0.0000 RESTRAINT = 0.0000
Ewald error estimate: 0.7391E-04
------------------------------------------------------------------------------
NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 43.43 PRESS = 0.0
Etot = 17975.0494 EKtot = 7272.5270 EPtot = 10772.2510
BOND = 115.2993 ANGLE = 298.2935 DIHED = 20.3217
1-4 NB = 17.1467 1-4 EEL = 15.8319 VDWAALS = 4446.4281
EELEC = 14593.3145 EHBOND = 0.0000 RESTRAINT = 164.8446
EAMBER (non-restraint) = 10607.4063
Ewald error estimate: 0.3756E-04
---------------------------------
NSTEP = 500 TIME(PS) = 21.000 TEMP(K) = 296.30 PRESS = -615.4
Etot = -202932.9197 EKtot = 49611.4538 EPtot = -252544.3735
BOND = 917.3575 ANGLE = 2751.2928 DIHED = 1526.4513
1-4 NB = 849.3287 1-4 EEL = -10168.0995 VDWAALS = 32388.4984
EELEC = -280809.2028 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 22885.2388 VIRIAL = 36032.8553 VOLUME = 989502.9883
Density = 0.8432
Ewald error estimate: 0.8011E-04
------------------------------------------------------------------------------
check COM velocity, temp: 0.001769 0.00(Removed)
NSTEP = 6000 TIME(PS) = 32.000 TEMP(K) = 298.47 PRESS = -579.2
Etot = -204770.1682 EKtot = 49974.2919 EPtot = -254744.4600
BOND = 911.8171 ANGLE = 2896.6200 DIHED = 1532.0473
1-4 NB = 846.2492 1-4 EEL = -10168.2911 VDWAALS = 32151.3854
EELEC = -282914.2879 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 23030.6541 VIRIAL = 34871.0267 VOLUME = 946774.3952
Density = 0.8812
Ewald error estimate: 0.1158E-03
------------------------------------------------------------------------------
vlimit exceeded for step 6192 ; vmax = 33.00017393388424
vlimit exceeded for step 6199 ; vmax = 91.63837208252728
Coordinate resetting cannot be accomplished,
deviation is too large
iter_cnt, my_bond_idx, i and j are : 4 1 5140 5139
-----------------------------------------------
This is my md2.in script.
--------------------
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 5.0,
cut = 9, ntr = 0,
ntc = 2, ntf = 2,
tempi = 298, temp0 = 298,
ntt = 3, gamma_ln = 1.0,
nstlim = 5000000, dt = 0.002,
ntpr = 500, ntwx = 500, ntwr = 5000
/
------------------------------
best,
Hwankyu.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue May 24 2005 - 18:53:00 PDT
