From: Sonu Kumar (sonu2kd_at_gmail.com)
Date: Fri Jul 22 2016 - 13:08:33 CDT
Thanks for helping me out. I will give it a try using both the methods.
And about "sir", I assure you it won't be happening again. It was just an
unintentional mistake.
On Fri, Jul 22, 2016 at 10:25 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:
> Hi Sonu,
>
> If this molecule is currently being simulated in vacuum, you could also
> try starting from a cubic box (lets say 40x40x40), and using pressure
> control to shrink the box down. I'm still not sure why you think the
> density means each molecule has that dimension though. I would rather
> imagine that there is a big mesh of these polymers, and that as a whole the
> mesh has a certain density, rather than individual chains being squeezed
> into a compact space.
>
> -Josh
>
> On 07/22/2016 10:37 AM, MEHRAN MB wrote:
> Hi Sonu,
>
> Basically, here are what Josh suggested:
> * There are also female users on this forum so it would better to use
> terms like "Dear Sir or Madam".
> * you need to increase the cutoffs length which seems it was a typo and
> you have already fixed that issue in your second email .CONF files.
> * you cannot (as long as I know) have simulation box smaller than your
> molecule size. The simulation box, at least, should be equal to [
> molecule_size + cuttoff length ]. This is the minimum size of the
> simulation box that you have to start with. Then, if you want to shrink
> your molecule, one way to do this is to do steering molecular dynamic using
> Collective Variable (colvar ) in NAMD. You can define radius of gyration as
> a variable and use harmonic restraint with moving centre to force your
> molecule to have target smaller radius of gyration. I have not done this
> before but it should be straight forward if you read Collective variable
> section in NAMD user guide. http://www.ks.uiuc.edu/Research/namd/2.10/ug/
>
>
> here is what you should probably do:
>
> add following two lines in your .CONF file
>
> colvars on
> colvarsConfig $name.in<http://name.in>
>
> which $name is name of collective variable configuration file.
> then in that file you should have something like
>
> colvar {
> name Rg # arbitrary name I chose Rg
> gyration {
> atoms {
> "select your atom here. look at
> http://www.ks.uiuc.edu/Research/namd/2.10/ug/node56.html#SECTION000133100000000000000
> }
> }
> }
>
> # look at
> http://www.ks.uiuc.edu/Research/namd/2.10/ug/node58.html#SECTION000135300000000000000
> harmonic {
> colvars Rg
> centers Ri # Ri your initial radius of gyration
> forceConstant 1.0
> targetCenters Rf # target radius of gyration
> targetNumSteps Ns # Number of steps for steering
> }
>
>
>
> hope it helps,
>
>
> kind regards,
> Mehran
>
> On Fri, Jul 22, 2016 at 7:58 AM, Sonu Kumar <sonu2kd_at_gmail.com<mailto:
> sonu2kd_at_gmail.com>> wrote:
>
>
>
> That was a mistake. Btw I don't quite get how to do what you suggest.
> Actually the molecule is larger than the pbc and its polymer.
> I have written both the conf files. Can you suggest what I must add. I
> have further elaborated it down.
>
> I have a polymer molecule of 1806 atoms with a density of 0.9.
> The molecule has been minimized for 5 ns and has dimensions 38*32*26.
>
> As per density I want to force it in a box of 25*25*25. However, upon
> wrapping it using pbctools and generating the pdb which is further used in
> the md simulation it is showing error probably because of bad contacts.
>
> Can you please suggest me how to perform md simulation on this molecule by
> forcing it in a box smaller than this. It shall be helpful if you can just
> tell the part of script that I must add in my configuration file. I have
> pasted the two configuration files I am using. Please tell what I should
> add in either of these two to achieve what I want.
>
> FIRST CONF FILE :
>
> #My configuration file for minimization of the initial pdb :(please tell
> what I should add):
>
> structure Poly.psf
> coordinates Poly.pdb
> outputName first
>
> set temperature 298
> firsttimestep 0
>
> paraTypeCharmm on
> parameters par_all22_prot.prm
>
> temperature $temperature
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.0
> switching on
> switchdist 10.0
> pairlistdist 14.0
>
>
> # Integrator Parameters
> timestep 2.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
> langevin on ;# do langevin dynamics
> langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen no ;# don't couple langevin bath to hydrogens
>
> restartfreq 500 ;# 500steps = every 1ps
> dcdfreq 500
> xstFreq 500
> outputEnergies 100
> outputPressure 100
>
> if {1} {
> minimize 1000
> reinitvels $temperature
> }
>
> run 2500000
>
>
>
>
>
>
>
>
> SECOND CONF FILE :(FOR PBC)
>
> structure final.psf
> coordinates minimized.pdb
> outputName sample
>
> set temperature 298
>
> firsttimestep 0
>
> margin 0
>
> paraTypeCharmm on
> parameters par_all22_prot.prm
>
> temperature 0
> reassignFreq 1000
> reassignIncr 10
> reassignHold 300
>
>
> if {1} {
> cellBasisVector1 24.954999923706055 0 0
> cellBasisVector2 0 24.954999923706055 0
> cellBasisVector3 0 0 24.954999923706055
> cellOrigin 12.9974365234375 13.76833438873291 11.9735107421875
> }
> wrapWater on
> wrapAll on
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 15.0
> switching on
> switchdist 13.0
> pairlistdist 17.5
>
>
> # Integrator Parameters
> timestep 1.0 ;# 2fs/step
> rigidBonds none ;# needed for 2fs steps
> #rigidTolerance 0.0005
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
>
> #PME (for full-system periodic electrostatics)
> if {1} {
> PME yes
> PMEGridSpacing 1.0
>
> #manual grid definition
> PMEGridSizeX 32
> PMEGridSizeY 32
> PMEGridSizeZ 32
> }
>
>
> langevin off ;# do langevin dynamics
> langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen no ;# don't couple langevin bath to hydrogens
>
> restartfreq 500 ;# 500steps = every 1ps
> dcdfreq 500
> xstFreq 500
> outputEnergies 100
> outputPressure 100
>
>
>
> if {1} {
> minimize 1000
> reinitvels $temperature
> }
>
> run 100000
>
>
>
>
>
>
>
>
>
>
>
>
>
>
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