From: saman amiri (saman_amiri00_at_yahoo.com)
Date: Thu Jun 30 2011 - 02:53:42 CDT
Regarding timestep decreasing, No, because it is only related to the MD calculation not for the minimization step.
Regarding the trick, I do not know what you exactly mean. The trick is about minimization. Your minimization steps and dcdfreq are 50000 and 250, respectively. Therefore, you should have a lot of frames even for the minimization process. Then I recommend you to follow the trick using the final snapshot of minimization.
Please also consider whether you have set the PBC parameters, correctly.
let me know if you have further questions.
________________________________
From: bharat gupta <bharat.85.monu_at_gmail.com>
To: saman amiri <saman_amiri00_at_yahoo.com>
Sent: Thursday, June 30, 2011 4:10 AM
Subject: Re: namd-l: Re: Equilibration
Hi, I want to ask can we do this what you said in your mail, for the minimization step. As after loading the psf file and then the .dcd file the number of frames doesnot increase in my case. Here are the minimization parameters that I am using:-
## JOB DESCRIPTION ##
#############################################################
# Minimization and Equilibration
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ../common/complex_ionized.psf
coordinates ../common/complex_ionized.pdb
set temperature 298
set outputname complex_minim
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters ../common/par_all27_prot_na.prm # you may need to specify a path
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
outputEnergies 100
outputPressure 100
#############################################################
## PBC PARAMETERS ##
#############################################################
# Periodic Boundary Conditions
cellBasisVector1 62.4 0.0 0.0
cellBasisVector2 0.0 51.6 0.0
cellBasisVector3 0.0 0.0 46.6
cellOrigin 8.3 69.6 -10.1
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 50000
reinitvels $temperature
run 50000 ;# 100 ps
On Thu, Jun 30, 2011 at 6:05 AM, saman amiri <saman_amiri00_at_yahoo.com> wrote:
Hi Bharat,
>
>
>As you can see, vdW interaction energy is out of order. The error is coming from too closeness of some atoms relative to each other. Upon finishing the minimization process, MD is crashed due to high velocity of those atoms which their Cartesian positions are too close to each other. Such an error is common when there are some coincidence of atoms position in the initial coordination file (pdb file).
>
>There are some ways to deal with the problem. One way is increasing minimization steps, but since minimization through 20000 steps is enough (I think), I recommend you to use the following trick:
>
>
>load the psf as well as final snapshot of your MD simulation. and then select those atoms which have a high velocity.
>
>
>set qwe [atomselect top "Write the controversial atoms index"]
>$qwe moveby {0.3 0.3 0.3}
>set qaz [atomselect top all]
>$qaz writepdb COOR.pdb
>
>
>now use the new pdb file (COOR.pdb) along with the previous psf file. Note you should first run a minimization step for about 5000 steps.
>
>if it dose not work, you have to decrease your timestep. Such an error is also common if you have atoms in your system with a high epsilon (for instance, Platinum and some other transition metals).
>
>
>hope this information is useful.
>
>
>
>Best,
>Saman
>
>
>
>
>
>
>________________________________
>From: bharat gupta <bharat.85.monu_at_gmail.com>
>To: namd-l_at_ks.uiuc.edu
>Sent: Wednesday, June 29, 2011 10:36 AM
>Subject: namd-l: Re: Equilibration
>
>
>I did equilibration after minimzation of 20000 steps , I am getting following errors during equilibration:-
>
>
>REASSIGNING VELOCITIES AT STEP 0 TO 0.5 KELVIN.
>ERROR: Atom 987 velocity is -4.97359e+007 1.4246e+007 -9.72224e+007 (limit is 12000)
>ERROR: Atoms moving too fast; simulation has become unstable.
>ERROR: Atom 1240 velocity is 3.36992e+009 6.45705e+009 -7.44682e+009 (limit is 12000)
>ERROR: Atom 1242 velocity is 14634 1513.07 -3196.57 (limit is 12000)
>ERROR: Atom 1245 velocity is -127634 -41660.9 39388.9 (limit is 12000)
>ERROR: Atom 1296 velocity is -2.8896e+009 -5.53689e+009 6.38561e+009 (limit is 12000)
>ERROR: Atoms moving too fast; simulation has become unstable.
>ERROR: Atom 963 velocity is 4.1778e+006 -1.19928e+006 8.16311e+006 (limit is 12000)
>ERROR: Atoms moving too fast; simulation has become unstable.
>ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG
>
>
>ENERGY: 0 3504.0840 2149.0188 952.3792 229.8267 -33464.9911 9999999999.9999 0.0000 0.0000 19.6729 9999999999.9999 0.4956 9999999999.9999 9999999999.9999 0.4956
>
>
>ERROR: Exiting prematurely; see error messages above.
>====================================================
>
>
>WallClock: 0.866000 CPUTime: 0.866000 Memory: 39.414063 MB
>Program finished.
>
>
>
>
>This is my equilibration configuration file:-
>
>
>structure ../common/complex_ionized.psf
>coordinates ../common/complex_ionized.pdb # not taken into account
>#binCoordinates ../common/complex_eq.coor # this one instead
>extendedSystem ../common/complex_eq.xsc
>outputname equilibrated
>cutoff 12.0
>exclude scaled1-4
>1-4scaling 1.0
>switching on
>switchdist 8.0
>DCDFreq 1000
>restartFreq 1000
>parameters ../common/par_all27_prot_na.prm
>paraTypeCharmm on
>
>
>berendsenPressure on
>berendsenPressureTarget 1.01325 # atmospheric pressure
>berendsenPressureCompressibility 4.57e-5 # liquid water
>berendsenPressureRelaxationTime 100.0
>berendsenPressureFreq 10
>
>
>temperature 0.5 # starting at 0.5 K
>reassignFreq 100
>reassignIncr 0.5
>reassignHold 300 # target T: 300 K
>numsteps 100000 # 100 ps, constant T the last 40 ps
>
>
>
>
>Can anybody tell be how to rectify the errors for those atoms.
>
>
>
>
>
>
>--
>
>Bharat
>Ph.D. Candidate
>Room No. : 7202A, 2nd Floor
>Biomolecular Engineering Laboratory
>Division of Chemical Engineering and Polymer Science
>Pusan National University
>Busan -609735
>South Korea
>Lab phone no. - +82-51-510-3680, +82-51-583-8343
>Mobile no. - 010-5818-3680
>E-mail : monu46010_at_yahoo.com
>
>
>
--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010_at_yahoo.com
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