RE: AW: AW: Sudden energy drop after minimization

From: Hyuntae Na (htna_at_hotmail.com)
Date: Tue Jun 26 2012 - 01:56:00 CDT

Hi, I agree that I should take longer minimization steps than 300. I tested the 20,000 minimization step. After its minimization iteration takes around 10,000 steps (the half of 20,000), the protein in the water box is almost reached to its minimum structure (its conformation does not change much except small fluctuation). By the way, after the minimization with 20,000 steps is fully done, the energy drop still exists. In this case, should the minimization be continued until there is no atom movement at all? One my question is if the MD simulation test example in the tutorial files, "namd-tutorial-files\1-3-box", runs with improper minimization, because its log also shows the same bond energy drop : 605.1437 -> 81.9360.
Thank you very much. Best regards,--Hyuntae From: norman.geist_at_uni-greifswald.de
To: htna_at_hotmail.com
CC: namd-l_at_ks.uiuc.edu
Subject: AW: AW: namd-l: Sudden energy drop after minimization
Date: Tue, 26 Jun 2012 08:40:39 +0200

“Regarding "300
minimization step", I selected the number by comparing the energy and
pressure variation between 100 - 2,000.”

 

I
have no idea what you mean. If you minimize correctly there is no more
variation in energies. And during minimization, there’s also no pressure
variation as it is constant volume and no temperature. Also, if the system isn’t
minimized correctly, there can be tensions in bonds and angles that unload with
the start of the molecular dynamic and so transfer to kinetic energy.

 

Arons
suggestion also sounds a good idea to check.

 

Norman Geist.

 

Von:
owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Hyuntae
Na

Gesendet: Montag, 25. Juni 2012 07:59

An: norman.geist_at_uni-greifswald.de

Cc: namd-l_at_ks.uiuc.edu

Betreff: RE: AW: namd-l: Sudden energy drop after minimization

 

Hi,

 

Thank you for you comment. The same situation happens in VMD tutorial file
too. If you look the log of "namd-tutorial-files\1-3-box",
the bond energy was decreased heavily also.

 

==========================================

LINE MINIMIZER BRACKET: DX 0.000711118 0.00142224 DU -15.5301 325.354 DUDX
-101999 59282 403961

PRESSURE: 100 -5584.57 -163.474 118.351 -163.474 -5545.59 104.068 118.351
104.068 -5585.23

GPRESSURE: 100 -6177 -188.545 78.1791 -127.553 -6102.01 191.88 203.577 164.188
-6078.77

Info: Initial time: 4 CPUs 0.0346818 s/step 0.200705 days/ns 267.297 MB memory

ETITLE:
TS BOND
ANGLE
DIHED
IMPRP
ELECT
VDW
BOUNDARY
MISC KINETIC
TOTAL
TEMP
POTENTIAL TOTAL3
TEMPAVG
PRESSURE
GPRESSURE VOLUME
PRESSAVG GPRESSAVG

ENERGY: 100
605.1437
733.6868
263.5997
11.0217
-23673.7631
915.4026
0.0000
0.0000 0.0000
-21144.9086
0.0000 -21144.9086
-21144.9086
0.0000
-5571.7963 -6119.2600
86856.0000 -5571.7963
-6119.2600

 

REINITIALIZING VELOCITIES AT STEP 100 TO 310 KELVIN.

TCL: Running for 2500 steps

PRESSURE: 100 -3391.8 -118.583 163.544 -118.583 -3457.46 240.736 163.544
240.736 -3391.52

GPRESSURE: 100 -3448.04 -186.276 91.045 -110.856 -3363.57 137.289 193.572
124.827 -3334.27

ENERGY: 100
81.9360
262.9427
263.6823
10.9727
-21774.1928
893.5803
0.0000
0.0000 4500.6962
-15760.3825 308.0595
-20261.0787 -15770.7326
308.0595 -3413.5938
-3381.9607 86856.0000
-3413.5938 -3381.9607

==========================================

 

As you see in the above capture, which is actually the copy from
"namd-tutorial-files\1-3-box\example-output\ubq_wb_eq.log" in the
tutorial files, the bond energy is decreased from 605.1437 to
81.9360. I am wondering if this is acceptable.

 

Regarding "300 minimization step", I selected the number by comparing
the energy and pressure variation between 100 - 2,000.

 

Best regards,

-- Hyuntae

 

 

 

>
From: norman.geist_at_uni-greifswald.de

> To: htna_at_hotmail.com

> CC: namd-l_at_ks.uiuc.edu

> Subject: AW: namd-l: Sudden energy drop after minimization

> Date: Mon, 25 Jun 2012 07:37:43 +0200

>

> Hi,

>

> as far as I can see, the total energy raised after minimization, what is

> expectable because of introduction of temperature. The energy you
mentioned

> is the bonded energy, and was decreased heavily, but I'm sure that comes
due

> to your way to short minimization. From the energies and the step times, I

> think you have a quit big system. Only 300 minimization steps is extremely

> too short. You should plot your total energy to see when it get nearly

> constant. Use the VMD namd plot plugin for that. I think an amount of

> 10.000-50.000 steps minimization is what you need.

>

> Norman Geist.

>

> > -----Ursprüngliche Nachricht-----

> > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im

> > Auftrag von Hyuntae Na

> > Gesendet: Samstag, 23. Juni 2012 02:56

> > An: namd-l_at_ks.uiuc.edu

> > Betreff: namd-l: Sudden energy drop after minimization

> >

> >

> > Hi All,

> >

> >

> > I faced one not understable case while running MD simullation. I want

> > to know if this is the known issue, or if there is a bug in my

> > configuration.

> >

> >

> > I set 300 iteration to minimize a protwin within a waterbox, and set

> > 250000 iterations (500 ps) for the MD simulation. In the mean time,

> > after the minimization step, the error drops drastically just before

> > the MD simulation starts. Following is the capture of its log:

> >

> >

> > ===============================================================

> >

> > LINE MINIMIZER BRACKET: DX 5.8119e-06 2.52175e-06 DU -0.0359273

> > 0.0067846 DUDX -11927.6 102.202 5360.57

> > LINE MINIMIZER REDUCING GRADIENT FROM 2.81013e+06 TO 2810.13

> > PRESSURE: 300 -6445.5 41.062 130.819 41.062 -6200.95 -15.5486 130.819
-

> > 15.5486 -6405.64

> > GPRESSURE: 300 -6275.61 83.2379 73.7774 72.8995 -6127.56 -41.0635

> > 98.9947 8.3979 -6236.38

> > Info: Benchmark time: 18 CPUs 0.913816 s/step 1057.66 days/ns 2548.52

> > MB memory

> > ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC
TOTAL

> > TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG

> > GPRESSAVG

> >

> > ENERGY: 300 7269.7257 6938.1628 3126.9451 85.7711 -260020.0382

> > 11411.5320 0.0000 0.0000 0.0000 -231187.9015 0.0000 -231187.9015 -

> > 231187.9015 0.0000 -6350.6979 -6213.1839 794942.8795 -6350.6979 -

> > 6213.1839

> >

> > REINITIALIZING VELOCITIES AT STEP 300 TO 310 KELVIN.

> > TCL: Running for 250000 steps

> > PRESSURE: 300 -3030.49 98.8762 52.9485 98.8795 -2881.76 -44.5797

> > 52.9495 -44.5823 -2989.42

> > GPRESSURE: 300 -3011.47 97.7027 79.4894 74.7973 -2851.13 -62.2207

> > 63.1423 -24.2313 -2948.84

> > ENERGY: 300 546.5513 1998.3257 3126.8298 85.6771 -238049.2276

> > 11143.8978 0.0000 0.0000 46586.0825 -174561.8635 309.2931
-221147.9460

> > -174561.8651 309.2931 -2967.2253 -2937.1491 794942.8795 -2967.2253 -

> > 2937.1491

> >

> > ===============================================================

> >

> >

> > The energy was 7269.7257, and temparature was 0.0000 just after the

> > minimization finished.

> >

> > However, the energy dropped as 546.5513 while the temparature became

> > 309.2931.

> >

> >

> >

> > I am wondering if this energy drop indicate the error of my
structure,

> > or not. I could observe the same situation in the NAMD tutorial
"namd-

> > tutorial-files/1-3-box" too.

> >

> >

> >

> > Thank you very much.

> >

> >

> >

> > Best regards,

> >

> > -- Hyuntae

>

                                               

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