Re: Implicit solvent lipid bilayer simulation in NAMD.

From: Subbarao Kanchi (ksubbu85_at_gmail.com)
Date: Wed Sep 17 2014 - 13:41:34 CDT

Hi Siva,
            Thank you for the reply. I read the namd manual and you are
correct it is not compatible with PME. I have not used the PME in my input
file.

Regards,
Subbu.

On Wed, Sep 17, 2014 at 11:53 PM, Siva Dasetty <sdasett_at_g.clemson.edu>
wrote:

> 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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