From: amit banerjee (amit_informatics_at_yahoo.com)
Date: Mon Jul 25 2011 - 07:42:35 CDT
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
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