[gmx-users] Regarding Glycine structure
Dilip H N
cy16f01.dilip at nitk.edu.in
Mon Mar 27 21:56:03 CEST 2017
i want to calculate RDF of glycine of Hn-OW, Hn-HW, Ha-OW, Ha-HW, Ca-OW,
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
2]Then, Using the index to calculate the pair correlation function for all
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)
Selection '0' parsed
Last frame 1000 time 10000.000
Analyzed 1001 frames, last time 10000.000
3] View the plot:
and if i view the obtained graphs in xmgrace i am getting only two kinds of
(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..??
<https://mailtrack.io/> Sent with Mailtrack
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..??
> 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
>> 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.
>> <https://mailtrack.io/> Sent with Mailtrack
>> 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:
>>>> I have a non zwitter ionic glycine molecule [NH2CH2COOH] in water, and
>>>> 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
>>>> 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
>>> and COOH can't coincide at any real pH value.
>>> 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
>>> Gromacs Users mailing list
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
> 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
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
With Best Regards,
More information about the gromacs.org_gmx-users