[gmx-users] distance restraint using bond with function 2

[Justin A. Lemkul]

On 1/7/10 3:48 PM, Feng Xu wrote:
> Hi, Justin, Thank you for your answer to my previous post. I just turned
> on the mail delivery from this list,
> so I reply you here, hope it is not so disruptive to this thread.
>
> My problem for the previous post is resolved, the problem is I should
> have modified files in ~username/gromacs/.., instead I modified
> files in ~username/gromacs-4.0.7/... .
>
> And regarding your advice:
> "Some unsolicited advice: surely you want a negative charge on the
> fluorine, and a bond between these two atoms, correct? "
>
> I am using a HF dimer potential developed by Cournoyer and Jorgensen in
> 1984. Both H and F have a +0.725e charge, there is a virtue site which
> carries all the negative neutralizing
> charges. My questions for you is : I don't need define the virtue site
> in .rtp file, right? And If I want the bond distance fixed, do I need

Virtual sites aren't defined in the .rtp, no, but you do need to define them if 
you want pdb2gmx to create them for you and write the correct .top and .gro 
including these virtual sites.  Read in the chapter about the implementation of 
virtual sites and .ddb file entries.

> put [ bond ] directive in the .rtp file?  Is a
> [ constraint ] in .itp file enough?
>

There are two approaches - either define [ constraints ] explicitly, or make a [ 
bonds ] entry in the .rtp file and define "constraints = all-bonds" in the .mdp 
file.

Also realize that ffgmx is deprecated (as cautioned by pdb2gmx, and probably 
somewhere in the manual), so there may be better force fields out there.

-Justin

> My intended application is using GROMACS to simulate a box of liquid HF.
>
> Thank you!
>
> Feng Xu (Postdoc at Iowa State University)
>
>
> On Thu, Jan 7, 2010 at 2:11 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     On 1/7/10 2:58 PM, Hans HEINDL wrote:
>
>         interstingly the distance restrain works well when one chooses
>         the bond
>         type 2 whatever this means physically
>
>         [bonds]
>
>         .
>         .
>         .
>         .
>         .
>         .
>         1       614     2       5,761   400000
>
>
>     What you've specified is not a distance restraint, it is just a
>     bond.  Bond types are explained in the manual (Chapter 5), which
>     should alleviate the "whatever this means" comment :)
>
>     -Justin
>
>
>         Hans
>
>
>     --
>     ========================================
>
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================