[gmx-users] Regarding Glycine structure

[Dilip H N]

i want to calculate RDF of glycine  of Hn-OW, Hn-HW, Ha-OW, Ha-HW,  Ca-OW,
 etc.,
So my commands were as follows...

1] To make indexes:-
gmx make_ndx -f md.gro -o Hn-OW.ndx

> del 2
Removed group 2 'SOL'
 > del 1
Removed group 1 'Water'
 > del 0
Removed group 0 'System'
> a H1 H2 H3 OW
Found xxx atoms with name H1 H2 H3 OW
0 HA1_HA2_OW : xxx atoms
> q


2]Then, Using the index to calculate the pair correlation function for all
frames:-
gmx rdf -f md.trr -s md.tpr -n Hn-OW.ndx -o rdf_Hn-OW.xvg

Available static index groups:
 Group  0 "HA1_HA2_OW" (xxx atoms)
Specify a selection for option 'ref'
(Reference selection for RDF computation):
(one per line, <enter> for status/groups, 'help' for help)
> 0
Selection '0' parsed
>cntrl+d
Last frame       1000 time 10000.000
Analyzed 1001 frames, last time 10000.000

3] View the plot:

xmgrace rdf_Hn-OW.xvg

and if i view the obtained graphs in xmgrace i am getting only two kinds of
graphs...ie.,
(a) for Hn-OW,Ha-OW etc, graphs are same for OW end indexing and
(b) for Hn-HW,Ha-HW etc., graphs are same for HW end indexing..

My doubts are..
1)What is this only two kinds of graphs am i getting..?? ,
2)I hope the above procedure to get RDF ie., commands 1] gmx make_ndx.....,
2] gmx rdf ..... 3] xmgrace..... are correct in accordance..
3)Or is there any mistake that i am doing..?? Can anybody rectify my
mistakes if any..??





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On Mon, Mar 27, 2017 at 10:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/27/17 8:50 AM, Dilip H N wrote:
>
>> 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..??
>>
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_
> Boundary_Conditions
>
> What you see on the VMD display is its best guess as to how things are
> connected.  That's not always right.  The topology is always right.  That's
> why trjconv exists.
>
> 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...
>>
>>
> You have provided no useful information about what these RDF plots are or
> how you acquired them, so there's no point for either of us in guessing.
> Maybe the distribution(s) that you're looking at simply don't vary as a
> function of protonation state.
>
> Is there any tutorials for these as an example..?? solving this would help
>> me a lot....
>>
>>
> It's an amino acid in water; it's as easy of a protein system as there is.
> There's nothing special about it that requires a tutorial.
>
> -Justin
>
>
>>   <https://mailtrack.io/> Sent with Mailtrack
>> <https://mailtrack.io/install?source=signature&lang=en&refer
>> ral=cy16f01.dilip at nitk.edu.in&idSignature=22>
>>
>>
>> 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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>>>
>>
>>
>>
> --
> ==================================================
>
> 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,

DILIP.H.N
Ph.D Student