AMBER Archive (2009)

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

From: parul sharma (sharmaparul7373_at_gmail.com)
Date: Fri Feb 20 2009 - 07:27:51 CST

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