From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Sat Oct 06 2007 - 11:24:47 CDT
Hi Ilya,
That's correct, as long as you use a velocity restart file (along with coordinates) you'll be ok (in theory :)).
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: Richard Wood <rwoodphd_at_yahoo.com>
Cc: NAMD list <namd-l_at_ks.uiuc.edu>
Sent: Saturday, October 6, 2007 11:30:25 AM
Subject: Re: namd-l: Charmm 22 vs Charmm 27
Yeah it makes sense, though it should not matter. A way to maintain temperature is to reinitialize ever so often. I don't believe I am reinitializing my velocities though because I provide a .restart.vel file.
On 10/5/07, Richard Wood <rwoodphd_at_yahoo.com> wrote:
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.
Looking for a deal?
Find great prices on flights and hotels with Yahoo! FareChase.
--
Ilya Chorny Ph.D.
____________________________________________________________________________________
Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more.
http://mobile.yahoo.com/go?refer=1GNXIC
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:20 CST