Restarting T-REMD with colvars

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Nov 04 2013 - 10:19:30 CST

Hello:
I wonder whether restarting a t-remd, particularly when colvars were
imposed, goes straigth as indicated in the example of namd2.9 (or namd2.10,
which I am currently using).

That is, job1.conf (for the first restarting) reads

*******************
source fold_alanin.conf
source [format $output_root.job0.restart10000.tcl ""]
set num_runs 20000

# prevent VMD from reading replica.namd by trying command only NAMD has
if { ! [catch numPes] } { source ../replica.namd }
*******************

while the shared simulation options read:

************
# shared simulation options for replica exchange

timestep 1.0

structure alanin.psf
coordinates unfolded.pdb

margin 10.0
stepspercycle 100
parameters alanin.params
exclude scaled1-4
1-4scaling 0.4
switching on
switchdist 7.0
cutoff 8.0
pairlistdist 10.0

langevin on
langevinDamping 10.0
*************

I can imagine (hope) that job1 scipt lets the simulation taking the
coordinates aftef execution of job0. However, what about if colvars were
imposed? For example, my shared simulation options read:

********************

# Shared simulation base and options
# for parallel tempering
# System P2i implicit NVT GB-SASA

# forcefield
paratypecharmm on
parameters ./par_all27_prot_lipid.prm

# molecules
structure ./P2i.psf
coordinates ./nvt-02.pdb

# constraints
colvars on ; # provide colvarsConfig (and colvarsINput if
restart)
colvarsConfig ./P2i_rmsd-colvars.in
colvarsInput ./nvt-02.restart.colvars.state

# about temperature
langevin on
langevinDamping 10.0

# Approximations
rigidBonds all ;# needed for 2fs/step
rigidTolerance 0.000001
exclude scaled1-4
cutoff 18.0
alphaCutoff 15.0 ;# for calc Born radii default 15.0
1-4scaling 1.0

# GBIS parameters
GBIS on
switching on
switchdist 15.0 ;# like in manual
pairlistdist 18.0 ;# like in manual
solventDielectric 80
ionConcentration 0.15
intrinsicRadiusOffset 0.09 ;# shrinks intrinsic atomic radii default 0.09
GBISDelta 1.0 ;# calc Born radii default 1.0
GBISBeta 0.8 ;# for cal Born radii default 0.8
GBISGamma 4.85 ;# for calc Born radii default 4.85

# Hydrophobic energy
sasa on
surfaceTension 0.006 ;# like in manual

# Multistep integrator parameters
timestep 2.0 ;# 2.0 fs/step
nonbondedFreq 2 ;# nonbonded forces every two steps
fullElectFrequency 4 ;# multiple of nonbondedFreq
stepspercycle 20 ;# redo pairlist every 20 steps

*******************

My concern is at least related to the flag

colvarsInput ./nvt-02.restart.colvars.state

Is it correct to leave that unchanged on restarting? Actaully, all that
above seems to work, also restarts, however, looking into what happens
those issues above came out outstandingly. Given the cost of a 32-replica
t-remd, I would like to understand it better.

Very grateful for advice

francesco pietra

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