it looks like your initial structure may have serious problems.
the EELEC, VDWAALS, and 1-3 change by thousands of kcal/mol.
at 20ps both of these are positive, and the total energy EPtot
has changed by 300,000 kcal/mol. This is really, really large.
Also, at the end of the 20ps the temperature is only 43K, not
298K like I think you are saying in your mail.
It looks like you combined 2 outputs- why is the 20ps energy
so different from the later one at 21ps? Maybe this is from
the productino run- but in any case the energies have again
changed by hundreds of thousands of kcal/mol. This is probably
not what should be happening.
I think you should try a different (probably slower) equilibration
protocol. Also, 2fs is at the edge of what is OK, with large
changes you may want to see if 1fs helps keep things more stable.
Look at the Amber tutorials and make plots of your energies,
temperature, pressure, etc during equilibration to see if it
really has equilibrated, and do not do the production run until
the other problems have been resolved.
Hwankyu Lee wrote:
> 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.
> -----------------------------------------------------------------------
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--
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
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Received on Tue May 24 2005 - 19:53:00 PDT
