AMBER Archive (2006)

Subject: Re: AMBER: NTT for production run

From: snoze pa (snoze.pa_at_gmail.com)
Date: Wed Mar 15 2006 - 11:03:22 CST

Dear AMBER Users,
 Thanks a lot for your help. As per your suggestions and AMBER
tutorials, I am using ntt=3.
I equilibrated the system for 200 ps (310 K) and now running 2 ns MD
full run. So far following are partial results for NTP MD full run.
All i can see from my output file a small flutuation in temperature.
Is it okie.(min 305 and Max 310K)
thanks in advance
snoze
 ------------------------------------------------------------------------------

 NSTEP = 99500 TIME(PS) = 399.000 TEMP(K) = 309.68 PRESS = 59.6
 Etot = -95326.4415 EKtot = 26613.1649 EPtot = -121939.6064
 BOND = 1045.1318 ANGLE = 2815.9238 DIHED = 3784.4208
 1-4 NB = 1161.0075 1-4 EEL = 15970.1721 VDWAALS = 13606.3426
 EELEC = -160322.6049 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 11509.0518 VIRIAL = 10965.1928 VOLUME = 422429.2128
                                                    Density = 1.0162
 Ewald error estimate: 0.2519E-04
 ------------------------------------------------------------------------------

check COM velocity, temp: 0.001643 0.00(Removed)

 NSTEP = 100000 TIME(PS) = 400.000 TEMP(K) = 310.38 PRESS = -43.2
 Etot = -95845.3141 EKtot = 26673.5457 EPtot = -122518.8598
 BOND = 1026.7292 ANGLE = 2676.8497 DIHED = 3772.1968
 1-4 NB = 1158.9358 1-4 EEL = 15971.0440 VDWAALS = 13741.7800
 EELEC = -160866.3953 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 11351.3538 VIRIAL = 11745.8865 VOLUME = 422626.3473
                                                    Density = 1.0157
 Ewald error estimate: 0.4184E-04
 ------------------------------------------------------------------------------

 NSTEP = 100500 TIME(PS) = 401.000 TEMP(K) = 305.88 PRESS = -39.6
 Etot = -95871.2284 EKtot = 26286.3268 EPtot = -122157.5552
 BOND = 1026.0251 ANGLE = 2743.6398 DIHED = 3769.7954
 1-4 NB = 1184.9697 1-4 EEL = 15994.8814 VDWAALS = 13740.3899
 EELEC = -160617.2566 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 11183.3195 VIRIAL = 11544.5781 VOLUME = 422500.6811
                                                    Density = 1.0160
 Ewald error estimate: 0.2840E-04
 ------------------------------------------------------------------------------

check COM velocity, temp: 0.002993 0.01(Removed)

 NSTEP = 101000 TIME(PS) = 402.000 TEMP(K) = 309.94 PRESS = 198.8
 Etot = -95713.5221 EKtot = 26635.9586 EPtot = -122349.4807
 BOND = 1053.1675 ANGLE = 2729.9318 DIHED = 3774.7142
 1-4 NB = 1146.1884 1-4 EEL = 15880.2441 VDWAALS = 13797.9301
 EELEC = -160731.6569 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 11405.5915 VIRIAL = 9592.8709 VOLUME = 422287.7057
                                                    Density = 1.0165
 Ewald error estimate: 0.1452E-03
 ------------------------------------------------------------------------------
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