AMBER Archive (2009)

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

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Fri Feb 20 2009 - 07:14:23 CST

Now for the bad news:

The output you sent, as far as I can see, is EXACTLY what you must
expect when changing from an NVT run to an NPT run.

You need to study, and read the archives in the list.
Think about what it means constant volume: it means constant volume !
so, the box would not change, of course.

Constant Pressure means that the system will TRY to maintain a constant
pressure, on average. This means that the volume will change, and so
will the density.

Adrian

parul sharma wrote:
> 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

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