Re: Pico scale to nanoscale simulation....alteration if .conf files required

From: Erik Nordgren (nordgren_at_sas.upenn.edu)
Date: Thu Jul 21 2011 - 20:22:25 CDT

Hi Amit,

To clarify... when you say "picoscale" and "nanoscale" are you referring to
the time-scale, i.e., you now want to do a simulation that runs for (say) 10
ns rather than 50 ps? If so, then really all you need to do is just
increase the number of steps in your "run" command... You might also want
to tweak the parameters for the frequency with which you save certain data
to your output files, but that will have no effect on the results, only the
amount of disk space you use.

BTW, I notice that in the attached script you started with 100,000 steps of
minimization (probably much more than needed) and then you suddenly began
your dynamics at your target temperature (rather than using some protocol
for gradually heating the system)... both of these choices seem unusual.

As for your question about the cutoff values, can you describe a bit more
about what you want to know?

-Erik 

-- 
C. Erik Nordgren, Ph.D.
University of Pennsylvania
On Sun, Jul 17, 2011 at 10:28 PM, amit banerjee
<amit_informatics_at_yahoo.com>wrote:
> Dear Friends,******
>
>                      Presently I am running a NAMD simulation in picoscale
> using the more or less default protocol as provided below. Kindly let me
> know what are the changes I should make in this .conf file to obtain a
> nanoscale simulation?****
>
>  ****
>
> My other question is what is the range of the cut off values can be used in
> the protocol for to perform a successful nanoscale simulation for a protein
> ranging from 250-500 amino acid in general.****
>
>  ****
>
> Picoscale .conf file applied:****
>
> ## SIMULATION PARAMETERS ##****
>
> #############################################################****
>
> # Input****
>
> paraTypeCharmm on****
>
> parameters ../common/par_all27_prot_lipid.inp ****
>
> temperature $temperature****
>
> ****
>
> # Force-Field Parameters****
>
> exclude scaled1-4****
>
> 1-4scaling 1.0****
>
> cutoff 12.****
>
> switching on****
>
> switchdist 10.****
>
> pairlistdist 13.5****
>
> ****
>
> # Integrator Parameters****
>
> timestep 2.0 ;# 2fs/step****
>
> rigidBonds all ;# needed for 2fs steps****
>
> nonbondedFreq 1****
>
> fullElectFrequency 2 ****
>
> stepspercycle 10****
>
> ****
>
> # Constant Temperature Control****
>
> langevin on ;# do langevin dynamics****
>
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps****
>
> langevinTemp $temperature****
>
> langevinHydrogen off ;# don't couple langevin bath to hydrogens****
>
> ****
>
> # Output****
>
> outputName $outputname****
>
> restartfreq 500 ;# 500steps = every 1ps****
>
> dcdfreq 250****
>
> outputEnergies 100****
>
> outputPressure 100****
>
> ****
>
> #############################################################****
>
> ## EXTRA PARAMETERS ##****
>
> #############################################################****
>
> # Spherical boundary conditions****
>
> sphericalBC off****
>
> sphericalBCcenter -1.42082428932 3.25120377541 2.19151377678****
>
> sphericalBCr1 26.0****
>
> sphericalBCk1 10****
>
> sphericalBCexp1 2****
>
> ****
>
> #############################################################****
>
> ## EXECUTION SCRIPT ##****
>
> #############################################################****
>
> # Minimization****
>
> minimize 100000****
>
> reinitvels $temperature****
>
> run 250000 ;# 50ps****
>
>  ****
>
>  ****
>
> Waiting for reply.****
>
>  ****
>
> Best Regards,****
>
> Amit Kumar Banerjee ****
>
> IICT****
>
> Hyderabad****
>
> ** **
>

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