[gmx-users] Re: choice of force field -reg

[Dr. Vitaly Chaban]

If you want to observe H-bond dynamics and do it with an atomistic
precision than, of course, you need an all-atom representation. United
atoms will still *effectively* account for H-bonding, if you are happy with
reduced precision.

Dr. Vitaly Chaban




On Wed, May 29, 2013 at 8:01 AM, Revthi Sanker <revthi.sanker at yahoo.com>wrote:

> Dear Sir,
> I would like to express my deepest gratitude for patiently reading my
> query. I am simulating the cholesteryl ester transfer protein ( the crystal
> structure has 4 bound lipids). I propose to study the inhibitor induced
> changes in the conformation of protein and the bound lipids. I am assuming
> unless I perform an all-atom  simulation, I will be missing out some
> crucial interactions like H-bond formation and breaking. Kindly let me if
> my understanding is wrong.
> Thank you so much once again for the reply,
> Revathi
>
> --- On *Tue, 28/5/13, Dr. Vitaly Chaban <vvchaban at gmail.com>* wrote:
>
>
> From: Dr. Vitaly Chaban <vvchaban at gmail.com>
> Subject: Re: choice of force field -reg
> To: "Revthi Sanker" <revthi.sanker at yahoo.com>, gmx-users at gromacs.org
> Date: Tuesday, 28 May, 2013, 4:14 PM
>
> without knowing full details of your simulated system and the goals you
> pose, I cannot advise anything more definite than I did before.
>
> if I were you and my system were yours, I would start with MARTINI FF.
>
> I wish you a success in your endeavor.
>
> Dr. Vitaly Chaban
>
>
>
>
> On Tue, May 28, 2013 at 6:11 PM, Revthi Sanker <revthi.sanker at yahoo.com<http://mc/compose?to=revthi.sanker@yahoo.com>
> > wrote:
>
>
>
> Dear Sir,
> Thank you so much for your reply. To be specific, my system has only four
> lipid moities- 2 cholesteryl oleates and 2 phosphotidyl cholines. But I was
> not able to get all atom paramters for these lipids from the lipid book(
> only united atom parameters were available). So I had resorted to using
> united atom for the whole system. But I am afraid if I am missing out on
> some crucial protein-drug interactions because of this united atom
> consideration.
> Kindly guide me in this regard.
> Thank you so much once again.
>
> Yours sincerely,
> Revathi
> M.S.Research Scholar
> Indian Institute of Technology Madras
> India
>
>
>