Re: Implicit solvent lipid bilayer simulation in NAMD.

From: Siva Dasetty (sdasett_at_g.clemson.edu)
Date: Wed Sep 17 2014 - 13:23:53 CDT

Hello Subbarao,

GBIS (implicit solvent) is not compatible with PME in NAMD. Please refer
the following link for further details.

http://www.ks.uiuc.edu/Research/namd/2.9/ug/node31.html

Thanks,
Siva

On Wed, Sep 17, 2014 at 1:04 PM, Subbarao Kanchi <ksubbu85_at_gmail.com> wrote:

> Dear all,
> 1) I am trying to run implicit solvent lipid bilayer
> simulation.I have use the fallowing namd configuration file to lipid
> bilayer simulation with GBIS but it collapsing (lipids are coming out of
> the bilayer) the lipid bilayer structure. Is any one know or experienced
> this problem.
> 2) Is the distance dependent dielectric method implemented in
> the NAMD. If yes, how to use it.
>
> I checked the mailing list and user guide but there is no use
> in this contest. I will appreciate any suggestions in this regards.
>
> namd configure file:
>
> structure not_water.psf
> coordinates not_water.pdb
> outputName eq_nvt_5ns
>
> set temperature 0
> set temperature1 303.15
>
> set cons 0
> # Input
> paraTypeCharmm on
> parameters par_all36_lipid.prm
> parameters test_petim.prm
>
> # NOTE: Do not set the initial velocity temperature if you
> # have also specified a .vel restart file!
> temperature $temperature1
>
>
> # Periodic Boundary Conditions
> # NOTE: Do not set the periodic cell basis if you have also
> # specified an .xsc restart file!
> if {1} {
> cellBasisVector1 136.475 0. 0.
> cellBasisVector2 0. 135.475 0.
> cellBasisVector3 0. 0. 200.0
> cellOrigin 0.0 0.0 0.0
> }
> wrapWater on
> wrapAll on
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
>
> GBIS on
> cutoff 16.0
> switching on
> switchdist 15.0
> pairlistdist 18.0
> # Integrator Parameters
> timestep 2.0 ;# 1fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 2
> fullElectFrequency 4
> stepspercycle 20
>
>
> #PME (for full-system periodic electrostatics)
> if {0} {
> PME yes
> PMEGridSpacing 1.0
> }
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
> langevinTemp $temperature1
>
> restartfreq 1000 ;# 1000steps = every 1ps
> dcdfreq 1000
> xstFreq 1000
> outputEnergies 1000
> outputPressure 1000
>
>
>
> run 2500000 ;# 5.0 ns
>
>
> Regards,
> Subbu.
>

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