AMBER Archive (2009)

Subject: [AMBER] Problem with NVT and NPT

From: parul sharma (sharmaparul7373_at_gmail.com)
Date: Fri Feb 20 2009 - 07:07:36 CST

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. 

-- 
With Best Regards

Parul Sharma
PhD Student, Durban University of Technology,
Durban,
South Africa
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