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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