I put wrong info about 20ps point. here, I attach 20ps energies again.
I really apologize for my mistake.
In 20ps, it has 299.88, which looks like reasonable temp.
could you look at this one more time?
-------------------------------
check COM velocity, temp: 0.002858 0.01(Removed)
NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 299.88 PRESS =
0.0
Etot = -201648.0152 EKtot = 50211.0109 EPtot =
-251859.0262
BOND = 898.2060 ANGLE = 2473.6478 DIHED =
1351.3450
1-4 NB = 826.9863 1-4 EEL = -10156.4761 VDWAALS =
32172.4335
EELEC = -280549.9268 EHBOND = 0.0000 RESTRAINT =
1124.7582
EAMBER (non-restraint) = -252983.7844
Ewald error estimate: 0.1165E-03
------------------------------------------------------------------------
------
best,
Hwankyu.
On May 24, 2005, at 1:51 PM, Carlos Simmerling wrote:
> 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.
>> ----------------------------------------------------------------------
>> -
>> The AMBER Mail Reflector
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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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>
>
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Received on Tue May 24 2005 - 19:53:00 PDT
