From: Mikhail Suyetin (msuyetin_at_gmail.com)
Date: Wed Dec 04 2019 - 09:51:10 CST
Dear Josh and Giacomo,
Many thanks for your advises. They really helped me.
I am doing simulations now, and I got results, that sodium ions are coming
over and leaving organosulfates. Is it fine to have such situation?
I believe, sodium ion should be really strongly attracted by Coulomb forces
to organosulfate.
Kind Regards,
Mikhail
On Tue, 19 Nov 2019 at 14:12, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:
> HI Mikhail,
>
> You'd also likely need to load in the standard lipid parameters
> (par_all36_lipid.prm), as what is in the toppar directory is an extension
> of the standard CHARMM parameter set. Giacomo's approach will get you the
> missing terms specific to SDS that aren't found in typical lipids.
>
> -Josh
>
>
>
> On 2019-11-19 10:57:36-07:00 Giacomo Fiorin wrote:
>
> Hello Mikhail, the stream file suggested by Josh includes both the
> topology template ("top" part) and the parameters ("par" part) of the
> CHARMM force field for detergents.
> You can extract what is enclosed between the two fields below:
> read para card append flex
> ...
> end
> And NAMD can read that as a "parameters" file.
> You may need to do the same for sodium as well, starting from
> "toppar_water_ions.str".
> Giacomo
>
> On Tue, Nov 19, 2019 at 12:04 PM Mikhail Suyetin <msuyetin_at_gmail.com>
> wrote:
>
>> Dear Josh,
>> Sorry for the late answer.
>> Great! Many thanks for this.
>> Another question, can you give me a hint where can I find a param file
>> (file with constants for bonds, angles, vdw interactions) for the
>> simulation of sodium dodecyl sulfate in NAMD?
>> Kind Regards,
>> Mikhail
>>
>> On Thu, 14 Nov 2019 at 17:46, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
>> wrote:
>>
>>> Hi Mikhail,
>>>
>>> SDS is in toppar_all36_lipid_detergent.str in the CHARMM 36 force field.
>>> The sodium would come from a solvate command to neutralize the system.
>>>
>>> -Josh
>>>
>>>
>>>
>>> On 2019-11-14 09:09:43-07:00 owner-namd-l_at_ks.uiuc.edu wrote:
>>>
>>> Dear All,
>>> Hope you are doing great.
>>> I would like to ask you, does anybody have files (psf, pdb, topology)
>>> for performing simulations for sodium dodecyl sulfate:
>>> https://en.wikipedia.org/wiki/Sodium_dodecyl_sulfate
>>> Kind Regards,
>>> Mikhail
>>>
>>>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Research collaborator, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>
>
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