[gmx-users] distance restraint using bond with function 2
fx2004 at gmail.com
Thu Jan 7 21:48:32 CET 2010
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 put [
bond ] directive in the .rtp file? Is a
[ constraint ] in .itp file enough?
My intended application is using GROMACS to simulate a box of liquid HF.
Feng Xu (Postdoc at Iowa State University)
On Thu, Jan 7, 2010 at 2:11 PM, Justin A. Lemkul <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
>> 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 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
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