Re: Equivalent of gromacs' "rdd" option

From: Fotis Baltoumas (fbaltoumas_at_biol.uoa.gr)
Date: Mon Jul 25 2016 - 10:26:05 CDT

Also, I just noticed, you use a temperature of 325 K (52 Celsius). Is
that high temperature necessary, for instance? If not, try using a more
"normal" temperature like 300 or 310 K. If lipid phase transitions is
what you're worried about, keep in mind that MARTINI lipids generally
have lower melting temperatures.

On 07/25/2016 06:08 PM, Fotis Baltoumas wrote:
>
> Hi,
>
> Unfortunately, I don't know of any workarounds. Theoretically, you
> could edit the part of the source that contains the rigidBonds
> function (that's where the SHAKE/RATTLE constraints algorithm is) and
> add LINCS-like code, but that would require more advanced knowledge of
> the NAMD code than what I can offer.
>
> You could try fooling around with the force magnitudes you use in the
> elastic network or the colvars code, maybe that would fix things
> somewhat. Also, if the simulation crashes occur after a while (for
> example, after the first 10 ns) and not immediately, you could split
> your big simulation to smaller ones and work with restart files.
>
> I hope you find a solution
>
> On 07/25/2016 10:56 AM, Marlon Sidore wrote:
>> Thanks.
>>
>> 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 colvars.
>>
>> 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
>> }
>>
>> #input
>> coordinates init_AqpZ.pdb
>> bincoordinates $inName.restart.coor
>> structure DimerAqpZ.psf
>>
>> paraTypeCharmm on
>> parameters martini-par/martini-protein-bonds.par
>> parameters martini-par/martini-protein-angles-cos.par
>> parameters martini-par/martini-protein-dihedrals.par
>> parameters martini-par/martini-all-nonb.par
>> parameters martini-par/martini-lipids-bonds-angles-dihedrals.par
>>
>> set temp325.0
>>
>> if {$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
>>
>> #Output
>> 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
>> colvars on
>> colvarsConfig ha8a.in <http://ha8a.in>
>> colvarsInput $inName.restart.colvars.state
>>
>> # CONSTANT-T
>> if {$temode == "t"} {
>> langevin yes ;# do langevin dynamics
>> langevinDamping 1 ;# damping coefficient(gamma)5/ps
>> langevinTemp $temp
>> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>> }
>>
>> # Constant Temperature Control ONLY DURING EQUILB
>> #reassignFreq 500; # reassignFreq: use this to
>> reassign velocity every 500 steps
>>
>> # CONSTANT-P
>> useGroupPressure no
>> useFlexibleCell yes
>> useConstantRatio yes
>>
>> if {$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
>> }
>>
>> #1-4's
>> exclude 1-2
>>
>> #Run
>>
>> run 60000000
>>
>>
>> Marlon Sidore
>>
>>
>> PhD Student
>> Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
>> CNRS - UMR7255
>> 31, Chemin Joseph Aiguier
>> 13402 cedex 20 Marseille
>> France
>>
>> 2016-07-22 18:05 GMT+02:00 Fotis Baltoumas <fbaltoumas_at_biol.uoa.gr
>> <mailto:fbaltoumas_at_biol.uoa.gr>>:
>>
>> 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 : fbaltoumas_at_biol.uoa.gr <mailto:fbaltoumas_at_biol.uoa.gr>
>> http://biophysics.biol.uoa.gr
>> http://bioinformatics.biol.uoa.gr
>> *******************************************
>>
>>
>
> --
> *******************************************
> 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 :fbaltoumas_at_biol.uoa.gr
> http://biophysics.biol.uoa.gr
> http://bioinformatics.biol.uoa.gr
> *******************************************

-- 
*******************************************
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 : fbaltoumas_at_biol.uoa.gr
http://biophysics.biol.uoa.gr
http://bioinformatics.biol.uoa.gr
*******************************************

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