Re: Charmm 22 vs Charmm 27

From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Fri Oct 05 2007 - 17:10:54 CDT

Ilya, When you restart, your "distribution" of velocities should behave as they did before your calculation stopped; in other words, when you restart, the velocity distribution should appear as if you never restarted the calculation, and should look as if it had been going continuously. Put another way, your "instantaneous" velocity for each atom when you restart should be the same velocity that rach had when your calculation ended. Does this make sense? Richard Richard L. Wood, Ph. D. University of Minnesota Dept. of Medicinal Chemistry, College of Pharmacy 717 Delaware St. SE Minneapolis, MN 55414-2959 rwoodphd_at_yahoo.com ----- Original Message ---- From: Ilya Chorny <ichorny_at_gmail.com> To: NAMD list <namd-l_at_ks.uiuc.edu> Sent: Friday, October 5, 2007 3:02:51 PM Subject: Re: namd-l: Charmm 22 vs Charmm 27 Below is configuration file. Does any one see any obvious mistakes? Can reinitializing the velocities when I restart a run cause the protein to fall apart? Thanks, Ilya structure addions.psf coordinates addions.pdb Bincoordinates Prot_free4.restart.coor Binvelocities Prot_free4.restart.vel ExtendedSystem Prot_free4.restart.xsc set temperature 310 set outputname Prot_free5 binaryoutput no #firsttimestep 0 ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters //winsc/share/namd/c31b1/par_all27_prot_lipid.prm #temperature $temperature # Force-Field Parameters exclude 1-4 1-4scaling 1.0 cutoff 12.0 switching off switchdist 10.5 pairlistdist 12.5 # 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 # Periodic Boundary Conditions #cellBasisVector1 117 0. 0. #cellBasisVector2 0. 117. 0. #cellBasisVector3 0. 0 92. #cellOrigin 10.09 9.73 -0.71 wrapAll on # PME (for full-system periodic electrostatics) PME yes PMEGridSizeX 128 PMEGridSizeY 128 PMEGridSizeZ 128 # Constant Pressure Control (variable volume) useGroupPressure yes ;# needed for rigidBonds useFlexibleCell yes useConstantRatio yes zeroMomentum yes langevinPiston yes langevinPistonTarget 1.01325 ;# in bar -> 1 atm langevinPistonPeriod 200. langevinPistonDecay 100. langevinPistonTemp $temperature # Output outputName $outputname restartfreq 500 ;# 500steps = every 1ps dcdfreq 500 xstFreq 500 outputEnergies 500 outputPressure 500 ############################################################# ## EXTRA PARAMETERS ## ############################################################# ############################################################# ## EXECUTION SCRIPT ## ############################################################# #Minimization #minimize 1000 # margin 2.5 reinitvels $temperature output NeRh50_free #run 2000000 ;# 2ns #run 1223500 ;# 2ns #run 906500 ;# 2ns #run 675500 ;# 2ns run 334000 ;# 2ns On 10/5/07, Ilya Chorny <ichorny_at_gmail.com> wrote: I am running a membrane protein simulation using the CHARMM 27 forcefield and I my protein seems to be falling apart. Could it be because I am using CHARMM27 instead of CHARMM22? I am also using TIP3 and POPE. Thanks, Ilya -- Ilya Chorny Ph.D. -- Ilya Chorny Ph.D. ____________________________________________________________________________________ Building a website is a piece of cake. Yahoo! Small Business gives you all the tools to get online. http://smallbusiness.yahoo.com/webhosting

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