[gmx-users] Regarding Glycine structure

Dilip H N cy16f01.dilip at nitk.edu.in
Mon Mar 27 14:50:30 CEST 2017

Thanks Justin,

But my doubts are..
1] after energy minimization of both glycine non zwitterionic form and
zwitterionic form with water, if i visualize it in vmd, the bond between
some of the water molecules are broken.. why is this so..??
2] and ran nvt,npt,md simulations respectively...and during analysis part i
am getting only similar two types of RDF graphs...why is this happening...i
have made all the indexing, etc., proper...

Is there any tutorials for these as an example..?? solving this would help
me a lot....

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On Sun, Mar 26, 2017 at 7:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 3/23/17 2:05 PM, Dilip H N wrote:
>> Hello,
>> I have a non zwitter ionic glycine molecule [NH2CH2COOH] in water, and in
>> the first step if i do the energy minimization and then visualizes the
>> mixture, the glycine is no more in its pure form as before instead it has
>> been converted to its zwitter ionic form [NH3CH2COO], and some Hydrogen
>> bonds with water are also broken. How can i solve these both issues..??
> Glycine didn't convert between forms.  That's impossible; bonds can't
> break or form in a molecular mechanical process.  The termini are exactly
> what you assigned them to be.  If you want them to be something else, you
> have to assign them as such with pdb2gmx.  Though you should note that NH2
> and COOH can't coincide at any real pH value.
> -Justin
> --
> ==================================================
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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With Best Regards,

Ph.D Student

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