From: MEHRAN MB (mb.mehran1_at_gmail.com)
Date: Fri Jul 22 2016 - 11:35:12 CDT
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 oncolvarsConfig $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
<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
<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> 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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