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

From: Erik Nordgren (nordgren_at_sas.upenn.edu)
Date: Tue Jul 26 2011 - 20:54:30 CDT

Hi Amit,

OK, so you already have a working simulation setup, having successfully run
it for 50ps, and now you want to run it longer. Well, as I said before,
aside from (obviously) increasing the number of steps in the "run" command,
there isn't anything else you would necessarily have to change in your
config file. You might want to increase "DCDfreq" (and similar parameters
that control how often various output data is saved) just to save space, but
that would depend on how much disk space you have, how long you want to run,
and perhaps most importantly, how much data you actually need in order to
get good statistics in whatever analysis you are planning to do afterward...
but only you can answer these questions.

Sorry if I'm misunderstanding you, but I'm not clear on what you mean with
your question... what defines a "decent" simulation? Which parameters do
you want to adjust? Is there something that you suspect may need to be
changed, and if so, why?

-Erik

On Mon, Jul 25, 2011 at 8:42 AM, amit banerjee
<amit_informatics_at_yahoo.com>wrote:

> Dear Erik,
> Thanks a lot for your kind help. I am referring the time
> scale only. My objective is to perform an equilibration and production
> dynamics analysis for a protein molecules (structure obtained using
> Modeller) ranging from 250-400 amino acid residues. I want to perform the
> simulation in a water box or in a water sphere using NAMD. I want to study
> the flexibility of the proteins (regions with maximum and minimum movements)
> as well as to perform a steered MD simulation at a later stage. The time
> scale should be in nano scale to obtain the structural flexibility (as i
> came to know from literature instead of pico seconds).
> Can you please help me out in adjusting the parameters for the dynamics run
> to obtain a decent nano scale simulation.
> The parameters I have used for preliminary testing is as follows:
>
>
>
> 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
>
>
> Looking forward for a reply.
> Best wishes,
> Amit
>
>
> --- On *Fri, 7/22/11, Erik Nordgren <nordgren_at_sas.upenn.edu>* wrote:
>
>
> From: Erik Nordgren <nordgren_at_sas.upenn.edu>
> Subject: Re: namd-l: Pico scale to nanoscale simulation....alteration if
> .conf files required
> To: "amit banerjee" <amit_informatics_at_yahoo.com>
> Cc: namd-l_at_ks.uiuc.edu
> Date: Friday, July 22, 2011, 6:52 AM
>
>
> 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<http://mc/compose?to=amit_informatics@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.****
>
>
>

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