AMBER Archive (2009)

Subject: Re: [AMBER] Problem with NVT and NPT

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Feb 20 2009 - 07:30:26 CST

that isn't an error, just information. did the simulation stop? if
yes, look for some other kind of error message.

On Fri, Feb 20, 2009 at 8:27 AM, parul sharma <sharmaparul7373_at_gmail.com> wrote:
> Dear Adrian,
>
> Thanks for your reply. I also want to perform MD under PME condition
> however, the problem is when i used the following input,
>
> &cntrl
> imin = 0, irest = 1, ntx = 7, ntb = 2, ntp = 1, pres0 = 1.0, taup = 2,
> cut = 10, tempi = 300.0, temp0 = 300.0,
> ntc=2, ntf=2, tol = 0.0001,
> ntt = 3, gamma_ln = 1.0,
> scee= 1.2, nstlim =250000, dt = 0.002,
> ntpr = 500, ntwx = 500, ntwr = 500, ntwe = 500,
> &ewald
> ew_type = 0 nfft1 = 25, nfft2 = 25, nfft3 = 20,
> a = 58.8103873, b = 47.4014584, c = 33.2335295,
> alpha = 90.0, beta = 90.0, gamma = 90.0
> order = 4, dsum_tol = 0.00001,
> /
>
> I got following error in my ouput:
>
> | Flags: MPI
> getting new box info from bottom of inpcrd
> | INFO: Old style inpcrd file read
> | peek_ewald_inpcrd: Box info found
> Could you please help me to sort this problem out?
>
> Thanks in advance
>
>
>
>
>> Dear All,
>>>
>>> I am doing MD calculations on my peptides in tip3p box (box information at
>>> the end of 1000.rst file,64.7369130 50.5592690 37.1945070 90.0000000
>>> 90.0000000 90.0000000), and for that initially i performed md for 100 ps
>>> under NVT condition (constant volume), and the box information remained
>>> same
>>> after simulation in it's 1001.rst output. After that i switched over to
>>> constant pressure condition using the following input
>>> &cntrl
>>> imin = 0, irest = 1, ntx = 7, ntb = 2, ntp = 1, pres0 = 1.0, taup = 2,
>>> cut = 10, tempi = 300.0, temp0 = 300.0,
>>> ntc=2, ntf=2, tol = 0.0001,
>>> ntt = 3, gamma_ln = 1.0,
>>> scee= 1.2, nstlim =250000, dt = 0.002,
>>> ntpr = 500, ntwx = 500, ntwr = 500, ntwe = 500,
>>> /
>>> However, although it is a constant pressure dynamics, the output shows
>>> inconsistency in values of pressure, volume and density as shown below.
>>>
>>> NSTEP = 249000 TIME(PS) = 1198.000 TEMP(K) = 295.51 *PRESS =
>>> 72.2*
>>> Etot = -25361.9761 EKtot = 5254.5535 EPtot =
>>> -30616.5296
>>> BOND = 28.5465 ANGLE = 96.6997 DIHED =
>>> 55.8232
>>> 1-4 NB = 26.4247 1-4 EEL = 488.8811 VDWAALS =
>>> 4251.4282
>>> EELEC = -35564.3330 EHBOND = 0.0000 RESTRAINT =
>>> 0.0000
>>> EKCMT = 2583.9130 VIRIAL = 2443.2495 *VOLUME =
>>> 90199.2591*
>>> *Density =
>>> 0.9995*
>>> Ewald error estimate: 0.4841E-04
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> NSTEP = 249500 TIME(PS) = 1199.000 TEMP(K) = 299.37 *PRESS =
>>> 286.1*
>>> Etot = -25178.7053 EKtot = 5323.2668 EPtot =
>>> -30501.9721
>>> BOND = 24.6498 ANGLE = 116.8027 DIHED =
>>> 41.1069
>>> 1-4 NB = 30.9753 1-4 EEL = 485.2544 VDWAALS =
>>> 4333.5439
>>> EELEC = -35534.3052 EHBOND = 0.0000 RESTRAINT =
>>> 0.0000
>>> EKCMT = 2635.0586 VIRIAL = 2077.6956 *VOLUME =
>>> 90221.7432*
>>> *Density =
>>> 0.9993*
>>> Ewald error estimate: 0.1397E-05
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> NSTEP = 250000 TIME(PS) = 1200.000 TEMP(K) = 303.02 *PRESS =
>>> 120.2*
>>> Etot = -25365.8305 EKtot = 5388.1310 EPtot =
>>> -30753.9615
>>> BOND = 32.4790 ANGLE = 104.0976 DIHED =
>>> 43.5360
>>> 1-4 NB = 24.6897 1-4 EEL = 472.6740 VDWAALS =
>>> 4326.3046
>>> EELEC = -35757.7425 EHBOND = 0.0000 RESTRAINT =
>>> 0.0000
>>> EKCMT = 2700.7686 VIRIAL = 2467.2198 *VOLUME =
>>> 89983.9445
>>> * *Density =
>>> 1.0019*
>>> Ewald error estimate: 0.1840E-04
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> A V E R A G E S O V E R 250000 S T E P S
>>>
>>> NSTEP = 250000 TIME(PS) = 1200.000 TEMP(K) = 299.93 *PRESS =
>>> 1.1
>>> * Etot = -25268.0235 EKtot = 5333.2193 EPtot =
>>> -30601.2428
>>> BOND = 28.7410 ANGLE = 99.4220 DIHED =
>>> 51.8274
>>> 1-4 NB = 27.3402 1-4 EEL = 476.8187 VDWAALS =
>>> 4235.8196
>>> EELEC = -35521.2117 EHBOND = 0.0000 RESTRAINT =
>>> 0.0000
>>> EKCMT = 2632.3824 VIRIAL = 2630.1747 *VOLUME =
>>> 90273.6798
>>> * *Density =
>>> 0.9987*
>>> Ewald error estimate: 0.1144E-03
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> R M S F L U C T U A T I O N S
>>>
>>> NSTEP = 250000 TIME(PS) = 1200.000 TEMP(K) = 3.05 *PRESS =
>>> 191.7*
>>> Etot = 88.6079 EKtot = 54.1744 EPtot =
>>> 73.9947
>>> BOND = 4.4096 ANGLE = 6.2604 DIHED =
>>> 4.4409
>>> 1-4 NB = 2.2522 1-4 EEL = 7.0925 VDWAALS =
>>> 75.7917
>>> EELEC = 117.6797 EHBOND = 0.0000 RESTRAINT =
>>> 0.0000
>>> EKCMT = 38.7054 VIRIAL = 375.0519 *VOLUME =
>>> 176.0771*
>>> *Density =
>>> 0.0019*
>>> Ewald error estimate: 0.8647E-04
>>>
>>> Also the box information which was there at the end of 1001.rst (after
>>> constant volume simulation), changed to 58.5551137 45.7313086 33.6427625
>>> 90.0000000 90.0000000 90.0000000 in 1002.rst and keeps on changing in
>>> the
>>> next outputs.
>>>
>>>
>> --
>> Dr. Adrian E. Roitberg
>> Associate Professor
>> Quantum Theory Project
>> Department of Chemistry
>>
>> Senior Editor. Journal of Physical Chemistry
>> American Chemical Society
>>
>> University of Florida PHONE 352 392-6972
>> P.O. Box 118435 FAX 352 392-8722
>> Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> With Best Regards
>
> Parul Sharma
> PhD Student, Durban University of Technology,
> Durban,
> South Africa
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

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