[gmx-users] POPC Berger lipids parameters for AMBER99sb

[Carlos Navarro]

Dear Justin,
To use a time step of 4fs(i clicked send by.mistake)

On Tue, Jul 9, 2019 at 7:59 AM Carlos Navarro <carlos.navarro87 at gmail.com>
wrote:

> Dear Justin,
> Thanks for the reply.
> I forgot to mention that indeed the reason of using Berger lipids is
> because there are united-atom. I'm planning on running computational
> electrophysiology simulations, and since my system is about 600k atoms I
> want to use vsites, as De Groot has been doing recently
> https://www.nature.com/articles/s41467-018-03179-y
> Best regards,
> Carlos
>
> On Tue, Jul 9, 2019 at 1:50 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 7/8/19 7:31 PM, Carlos Navarro wrote:
>> > Dear gmx-users,
>> > I was wondering if someone can share the Berger parameters for POPC for
>> > Amber99sb (and I they can share also a .pdb .gro file will be even
>> better).
>> > I found several for gromos, but I need them form AMBER99sb.
>>
>> Berger parameters are united-atom and designed for use with GROMOS. I
>> know some people have combined them with various protein force fields
>> with varying success, but I would not do that. Berger parameters are
>> wildly outdated and much better force fields exist. In your case, use
>> Slipids, which are specifically designed to be compatible with AMBER.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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> --
>
> ----------
>
> Carlos Navarro Retamal
>
> Bioinformatic Engineering. PhD
>
> Postdoctoral Researcher in Center for Bioinformatics and Molecular
> Simulations
>
> Universidad de Talca
>
> Av. Lircay S/N, Talca, Chile
>
> T: (+56) 712201 <//T:%20(+56)%20712201> 798
>
> E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl
>
-- 

----------

Carlos Navarro Retamal

Bioinformatic Engineering. PhD

Postdoctoral Researcher in Center for Bioinformatics and Molecular
Simulations

Universidad de Talca

Av. Lircay S/N, Talca, Chile

T: (+56) 712201 <//T:%20(+56)%20712201> 798

E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl