Re: Equivalent of gromacs' "rdd" option

From: Marlon Sidore (
Date: Mon Jul 25 2016 - 02:56:06 CDT


I will fool around with margin, with hopes that it reduces the crashes.

My simulations are already running (and crashing) at 10fs, probably since I
am also using the colvars module and putting more forces on the protein
bonds. There is no workaround to the absence of LINCS for all bonds then ?
Because the main thing about using NAMD with MARTINI here is using the

Attaching my configuration parameters below:
#Run namd in the folder
set pvmode "p" ;#p to activate pression control
set temode "t" ;#t to activate temperature control
set restart 1 ;#0 for new sim, 1 for continuation

set inName ha8a-411
set outName ha8a-412

proc get_first_ts { xscfile } {
  set fd [open $xscfile r]
  gets $fd
  gets $fd
  gets $fd line
  set ts [lindex $line 0]
  close $fd
  return $ts

coordinates init_AqpZ.pdb
bincoordinates $inName.restart.coor
structure DimerAqpZ.psf

paraTypeCharmm on
parameters martini-par/martini-protein-bonds.par
parameters martini-par/martini-protein-angles-cos.par
parameters martini-par/martini-protein-dihedrals.par
parameters martini-par/martini-all-nonb.par
parameters martini-par/martini-lipids-bonds-angles-dihedrals.par

set temp 325.0

if {$restart == 1} {
  binvelocities $inName.restart.vel
  extendedSystem $inName.restart.xsc
  set currenttimestep [get_first_ts $inName.restart.xsc]
  COMMotion yes
} else {
  temperature $temp
  set currenttimestep 0
  COMmotion no

firsttimestep $currenttimestep

#cutoff et martini
cutoff 12.0
switching on
switchdist 9.0
cosAngles on
martiniSwitching on
dielectric 15.0
pairlistdist 24.0
stepspercycle 20
margin 2.0 ;#échantillonnage de l'espace
splitpatch hydrogen

#Boundary conditions
cellBasisVector1 200.0 0.0 0.0
cellBasisVector2 0.0 208.0 0.0
cellBasisVector3 0.0 0.0 93.0
cellOrigin 0.0 0.0 0.0
wrapWater on
wrapAll on

binaryoutput yes ;#binary plus précis que pdb : utiliser flipbinpdb
pour utiliser ces fichiers en sortie
binaryrestart yes
outputname $outName
restartname $outName.restart
restartfreq 10000

DCDfile $outName.dcd
DCDfreq 10000

outputTiming 10000 ;#CPU & wallclock times, energy and pressure
output to stdout
outputEnergies 10000
outputPressure 10000

XSTfile $outName.xst
XSTFreq 1

timestep 10.0

#Constraints and restraints
constraints on
fixedAtoms off ;# switch to off after PR simulation
extraBonds yes ;#For elastic network
extraBondsFile ElastDimer.dat #For elastic network
consref init_AqpZ.pdb
conskfile harmonichelicesBAS.cnst
conskcol O
consexp 2
constraintScaling 1

colvars on
colvarsInput $inName.restart.colvars.state

if {$temode == "t"} {
langevin yes ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient(gamma)5/ps
langevinTemp $temp
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Constant Temperature Control ONLY DURING EQUILB
#reassignFreq 500; # reassignFreq: use this to
reassign velocity every 500 steps

useGroupPressure no
useFlexibleCell yes
useConstantRatio yes

if {$pvmode == "p"} {
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
#one may need to bump up the pressure constants at first
langevinPistonPeriod 2000 ;#usually 2000
langevinPistonDecay 1000 ;#usually 1000
langevinPistonTemp $temp

exclude 1-2


run 60000000

Marlon Sidore

PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille

2016-07-22 18:05 GMT+02:00 Fotis Baltoumas <>:

> Hello,
> The quick answer is no, there isn't any equivalent of -rdd in Namd. But
> you could try replicating its effect by fooling around with parameters that
> determine the system partition size, such as "margin" (manually set its
> value in the configuration file, start with low values and increase until
> the crashes stop). Although, until you give us your configuration
> parameters and the actual error you get, I cannot be of more help.
> Having said that, it should be pointed out that the NAMD version of
> protein topology/parameters of MARTINI is problematic at best. The main
> issue is that, since NAMD doesn't implement any equivalent for LINCS
> (constraints for all bonds, not just those of hydrogens), all bond
> constraints were modeled as regular bonds but with very high force constant
> values, which leads to a lot of crashes when timesteps of 20 fs or above
> are used. If you're using such a value, try lowering the timestep to 10 fs
> and see if that solves your issue. Most crashes I have had when using
> MARTINI with NAMD to simulate proteins were solved by doing that (the lipid
> parameter implementation was more successful since no constraints needed to
> be defined).
> Hope that helps
> On 07/22/2016 06:12 PM, Marlon Sidore wrote:
>> Hello,
>> I am simulating membrane proteins with the martini forcefield in NAMD but
>> have been struggling with random crashes from the beginning of this
>> journey
> --
> *******************************************
> Fotis A. Baltoumas
> Phd Candidate, Bioinformatics Postgraduate Programme
> Department of Cell Biology and Biophysics
> Faculty of Biology, University of Athens
> Panepistimiopolis, Athens 157 01, GREECE
> --------------------------------------
> email :
> *******************************************

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