Re: discrete energy value after restart

From: Chris Harrison (charris5_at_gmail.com)
Date: Sun Jan 23 2011 - 10:00:07 CST

Dear Kang Hee,

If you perform a single namd run containing:

minimize 10
run 10

Do you find the last min step and first MD step to differ?

I suspect your velocities are being resassigned. This can occur when
performing a restart and not using the standard restart procedure in namd,
or when issuing a command to re-evaluate the velocities between the
minimize and run commands (ie reassigning the temperature).

Best,
Chris

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                          Voice: 217-244-1733
http://www.ks.uiuc.edu/~char              Fax:   217-244-6078
Kang Hee Cho <gkdkang_at_gmail.com> writes:
> Date: Fri, 21 Jan 2011 12:25:46 +0900
> From: Kang Hee Cho <gkdkang_at_gmail.com>
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: discrete energy value after restart
> 
> Hi, everyone.
> 
> I am trying to simulate a protein using NAMD, but I am having a
> problem with discrete energy value.
> 
> I want to simulate protein with NAMD 3 steps.
> First, minimization. (all atoms are fixed except backbone)
> Second, minimization with the backbone of the protein fixed.
> Third, execution with the backbone fixed.
> 
> I restarted my protein but I found that the energy of the last step of
> the first minimization and the starting step of the second one is
> different.
> 
> Last step of first minimization
> ETITLE:      TS           BOND          ANGLE          DIHED
> IMPRP               ELECT            VDW       BOUNDARY           MISC
>        KINETIC               TOTAL           TEMP      POTENTIAL
>   TOTAL3        TEMPAVG
> ENERGY: 1000 58.4236 481.1728 286.8849 4.8477 -2588.3444 -91.7916
> 0.0000 0.0000 0.0000 -1848.8071 0.0000 -1848.8071 -1848.8071 0.0000
> 
> Starting step of second simulation
> ENERGY: 1000 237.1904 2565.7394 553.0368 0.6446 -4628.9693 6496.4700
> 0.0000 0.0000 0.0000 5224.1119 0.0000 5224.1119 5224.1119 0.0000
> 
> I have tried a lot of things, but I don't know what to do.
> Any help would be appreciated.
> 
> Cho
> 
> The molecule “qsu.psf”, “qsu.pdb” were used in the simulation.
> The file “qsu_nw_eq.conf” was written for the first step and the file
> “qsu_nw_eq2.conf” was for the second step
> 
> Another question is why I have to minimize whenever fixed atoms change
> their position?
> 
> ------------------------------------------
> "qsu_nw_eq.conf"
> 
> structure          qsu.psf
> coordinates        qsu.pdb
> 
> set temperature    300
> set outputname     qsu_nw_eq
> 
> firsttimestep      0
> 
> # Input
> paraTypeCharmm     on
> parameters          par_all22_prot.inp
> temperature         $temperature
> 
> # Force-Field Parameters
> exclude             scaled1-4
> 1-4scaling          1.0
> cutoff              13.5
> switching           on
> switchdist          10.
> pairlistdist        16.5
> 
> # Integrator Parameters
> timestep            2.0  ;# 2fs/step
> rigidBonds          all  ;# needed for 2fs steps
> nonbondedFreq       1
> fullElectFrequency  2
> stepspercycle       10
> 
> # Output
> outputName          $outputname
> 
> restartfreq         500     ;# 500steps = every 1ps
> dcdfreq             50
> outputEnergies      100
> outputPressure      100
> 
> # Fixed Atoms Constraint
> fixedAtoms          on
> fixedAtomsFile      qsu_nw_eq.ref ;# all atoms are fixed except backbone
> 
> fixedAtomsCol       B
> 
> # Minimization
> minimize            1000
> 
> --------------------------------------
> "qsu_nw_eq2.conf"
> 
> structure          qsu.psf
> coordinates        qsu.pdb
> bincoordinates     qsu_nw_eq.coor
> binvelocities      qsu_nw_eq.vel
> #extendedSystem
> 
> set outputname     qsu_nw_eq2
> firsttimestep      1000
> 
> # Input
> paraTypeCharmm     on
> parameters          par_all22_prot.inp
> 
> # Force-Field Parameters
> exclude             scaled1-4
> 1-4scaling          1.0
> cutoff              13.5
> switching           on
> switchdist          10.
> pairlistdist        16.5
> 
> # Integrator Parameters
> timestep            2.0  ;# 2fs/step
> rigidBonds          all  ;# needed for 2fs steps
> nonbondedFreq       1
> fullElectFrequency  2
> stepspercycle       10
> 
> # Output
> outputName          $outputname
> restartfreq         500     ;# 500steps = every 1ps
> dcdfreq             50
> outputEnergies      100
> outputPressure      100
> 
> # Fixed Atoms Constraint
> fixedAtoms          on
> fixedAtomsFile      qsu_nw_eq2.ref ;# backbone of the protein fixed
> 
> fixedAtomsCol       B
> 
> # Minimization
> minimize            1000
> run 1000
> ---------------------------------------------
> 

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