From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Nov 19 2019 - 11:56:56 CST
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
And NAMD can read that as a "parameters" file.
You may need to do the same for sodium as well, starting from
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,
> On Thu, 14 Nov 2019 at 17:46, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
>> 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.
>> 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:
>> Kind Regards,
-- 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
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2020 - 23:17:12 CST