Fwd: GaMD config file

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Jan 21 2020 - 03:26:23 CST

As far as I can understand, from previous normal MD production:
final .coor = .pdb file
cellOrigin and cellBasis
# temperature control
temperature 310
langevin on
langevinTemp 310
langevinDamping 5
langevinHydrogen off

# constant pressure control
useGroupPressure yes
useFlexibleCell no
UseConstantArea no
useConstantRatio no
LangevinPiston on
LangevinPistonTarget 1.01325
LangevinPistonPeriod 200
LangevinPistonDecay 100
LangevinPistonTemp 310

# integrator
timestep 2.0 # 2.0 fs/step
nonbondedFreq 1 # nonbonded forces every step
fullElectFrequency 5 # PME only every five step
stepspercycle 20 # redo pairlist every 20 steps

# Approximations
# rigidBonds all # needed for 2fs/step
rigidBonds water
rigidTolerance 0.000001
exclude scaled1-4
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 13.5 # cutoff +3.5
margin 3
1-4scaling 1.0
PME yes


---------- Forwarded message ---------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Mon, Jan 20, 2020 at 10:43 PM
Subject: GaMD config file
To: NAMD <namd-l_at_ks.uiuc.edu>

I am asking advice from people familiar with GaMD.

When starting GaMD from a system already subjected to normal MD production,
which part of the normal MD config file should be retained in addition to
the GaMD parameters

accelMD on
accelMDdihe on
accelMDdual on
accelMDOutFreq 10
accelMDG on
accelMDGcMDPrepSteps ....
accelMDGcMDSteps ....
accelMDGEquiPrepSteps ....
accelMDGEquiSteps .......
# accelMDGRestart on
accelMDGRestartFile GaMD.game

or GaMD is intended not to take advantage of previous MD production? I
tried a combination of MD and GaMD parameters. It goes on, but it seems to
create some confusion. with .restart.coor .restart.vel .restat.xsc files in
addition to the .gam file

francesco pietra

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2020 - 23:17:12 CST