[gmx-users] gromacs.org_gmx-users Digest, Vol 159, Issue 125

suniba shuaib suniba88chemistry at gmail.com
Mon Jul 31 10:41:59 CEST 2017 

*Hi all,>> I am calculating the RDF from a particular residue to a
particular> glycine molecule. I created an index file for both to do this.
My> simulation box is 1.5nm, but the RDF values are in the range of
2nm-3nm.> I have viewed my trajectory and all the components stay inside
the box.> Please could someone tell me how to overcome this issue? My
command line> is below:>> gmx rdf -f output.xtc -s input.tpr -n index.ndx
-o rdf.xvg -b 0 -e 60000> -ref -sel -bin 0.5 -norm rdf>> Akash> --*

*Hi *
*Akash*
*Are you sure your simulation box is 1.5 nm? This sounds bit strange and
too small. What is the length of your protein or no. of amino acids. I am
afraid you are talking about the distance from edge to protein is 1.5nm. *

*Regards*
*Suniba*

On Mon, Jul 31, 2017 at 1:58 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

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> Today's Topics:
>
>    1. Re: Question on force field (YanhuaOuyang)
>    2. gmx mdmat calculation of heavy atoms of two side chains
>       (????? ?????????)
>    3. RDF Values (Pandya, Akash)
>    4. Re: RDF Values (saima kalsoom)
>    5. hole in the simulation box (edesantis)
>    6. Re: RDF Values (spss4 at iacs.res.in)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 31 Jul 2017 10:54:37 +0800 (CST)
> From: YanhuaOuyang <15901283893 at 163.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Question on force field
> Message-ID: <18244f50.3a1e.15d969118bb.Coremail.15901283893 at 163.com>
> Content-Type: text/plain; charset=us-ascii
>
> Dear Justin, <br/> Thank you very much. I get it now.<br/><br/>Best
> regards,<br/>Ouyang
> At 2017-07-31 10:46:10, "Justin Lemkul" <jalemkul at vt.edu> wrote:
> >
> >
> >On 7/30/17 8:58 PM, YanhuaOuyang wrote:
> >> Hi,
> >>   I have run a protein MD simulation and choose a force field "8:
> CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) ". I wonder
> that whether the CHARMM27 all-atom force field here is equal to the
> CHARMM22/CMAP
> >>
> >
> >Well, not "equal" but it means that the "CHARMM27" files include C22/CMAP
> for
> >proteins.  There is no such thing as a CHARMM27 protein force field.  The
> C27
> >nucleic acid and lipid parameters came out at the same time as the
> C22/CMAP
> >protein force field, and got somewhat unfortunately lumped together in
> nomenclature.
> >
> >-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
> >
> >==================================================
> >--
> >Gromacs Users mailing list
> >
> >* Please search the archive at http://www.gromacs.org/
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> ------------------------------
>
> Message: 2
> Date: Mon, 31 Jul 2017 14:19:07 +0900
> From: ????? ?????????   <b.mijiddorj at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] gmx mdmat calculation of heavy atoms of two side
>         chains
> Message-ID:
>         <CABgRApuA3d+Vi=XzoBshixqXOypvPx0Ady0bP_aoE0p3O7JFzw at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear gmx users,
>
> I would like to know about the hydrophobic interaction between heavy atoms
> of side chains in different chains of peptides. How can I use mdmat tool
> for this calculation? I  separately indexed all heavy atoms but mdmat use
> only one index group in the calculation. I re-integrated all separate
> groups into a group. Calculation result came out only two side chain
> distance image.
> If you have any suggestion please help me?
>
>
> Best regards,
> Mijee
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 31 Jul 2017 07:29:19 +0000
> From: "Pandya, Akash" <akash.pandya.15 at ucl.ac.uk>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: [gmx-users] RDF Values
> Message-ID:
>         <VI1PR0101MB2429BBD2A051AD28F2ED8996EBB20 at VI1PR0101MB2429.
> eurprd01.prod.exchangelabs.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi all,
>
> I am calculating the RDF from a particular residue to a particular glycine
> molecule. I created an index file for both to do this. My simulation box is
> 1.5nm, but the RDF values are in the range of 2nm-3nm. I have viewed my
> trajectory and all the components stay inside the box. Please could someone
> tell me how to overcome this issue? My command line is below:
>
> gmx rdf -f output.xtc -s input.tpr -n index.ndx -o rdf.xvg -b 0 -e 60000
> -ref -sel -bin 0.5 -norm rdf
>
>
> Akash
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 31 Jul 2017 07:57:51 +0000 (UTC)
> From: saima kalsoom <genious_chemist at yahoo.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] RDF Values
> Message-ID: <1848591093.2375411.1501487871322 at mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> hi dear!can anyone please suggest me what does it mean."In chosen Force
> field there is no residue type for QLN"there was no QLN in our origin file.
> There is always a problem when i select any force field.regards
>
>     On Monday, 31 July 2017, 12:29, "Pandya, Akash" <
> akash.pandya.15 at ucl.ac.uk> wrote:
>
>
>  Hi all,
>
> I am calculating the RDF from a particular residue to a particular glycine
> molecule. I created an index file for both to do this. My simulation box is
> 1.5nm, but the RDF values are in the range of 2nm-3nm. I have viewed my
> trajectory and all the components stay inside the box. Please could someone
> tell me how to overcome this issue? My command line is below:
>
> gmx rdf -f output.xtc -s input.tpr -n index.ndx -o rdf.xvg -b 0 -e 60000
> -ref -sel -bin 0.5 -norm rdf
>
>
> Akash
> --
> 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
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>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 31 Jul 2017 10:14:54 +0200
> From: edesantis <edesantis at roma2.infn.it>
> To: Gmx users <gmx-users at gromacs.org>
> Subject: [gmx-users] hole in the simulation box
> Message-ID: <ebb2c1370cb1e60091753019723443f0 at imap.roma2.infn.it>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
> Hi gromacs users,
>
> I am trying to simulate a crystal supershell (5x5x5 unit cells) with
> martini ff in gromacs 5.
>
> I build the system in aa representation, then I converted it in CG using
> the martinize.py script,
>
> following the tutorial, I've done a brief equilibration in water, the
> after the solvatation of the system with non-polarizable water, I've
> perform another energy minimization followed by the equilibration.
>
> then I've performed md simulation in the NVT ensemble.
>
> It happened that during the first steps of md, an empty (no protein no
> water) hole was created in my simulation box. during the md simulation
> the hole size became bigger (this hole doesn't appear if I do the
> simulation in NPT, but I'd prefer to avoid this ensemble since a dynamic
> volume of the box could alter the reticolar parameters of my crystal),
>
> I've tried to calculate forces using different algorithms but the hole
> is formed every time.
>
> the density of my system is 1.1 times the experimental one.
>
> Do you have an idea of the reason why I found this hole? do you have any
> suggestion to avoid its formation??
>
>
> thank you in advance,
> regards
> Emiliano De Santis
>
> --
> Emiliano De Santis
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 31 Jul 2017 13:45:20 +0530
> From: spss4 at iacs.res.in
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] RDF Values
> Message-ID:
>         <20170731134520.Horde.dOS5QlvVEUAGb_jE4JgpVg3 at mailweb.iacs.res.in>
> Content-Type: text/plain; charset=UTF-8; format=flowed; DelSp=Yes
>
>   I think you can use -cut 0 -rmax 1.5 this will give you the RDF upto 1.5
> nm.----- Message from "Pandya, Akash" <akash.pandya.15 at ucl.ac.uk>
> ---------
> ? ? Date: Mon, 31 Jul 2017 07:29:19 +0000
> ? ? From: "Pandya, Akash" <akash.pandya.15 at ucl.ac.uk>
> Reply-To: gmx-users at gromacs.org
> Subject: [gmx-users] RDF Values
> ? ? ? To: gmx-users at gromacs.org
>
> > Hi all,
> >
> > I am calculating the RDF from a particular residue to a particular
> > glycine molecule. I created an index file for both to do this. My
> > simulation box is 1.5nm, but the RDF values are in the range of 2nm-3nm.
> > I have viewed my trajectory and all the components stay inside the box.
> > Please could someone tell me how to overcome this issue? My command line
> > is below:
> >
> > gmx rdf -f output.xtc -s input.tpr -n index.ndx -o rdf.xvg -b 0 -e 60000
> > -ref -sel -bin 0.5 -norm rdf
> >
> > Akash
> > --
> > 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
> >
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> > or send a mail to gmx-users-request at gromacs.org.
>
> ----- End message from "Pandya, Akash" <akash.pandya.15 at ucl.ac.uk> -----
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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>
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> End of gromacs.org_gmx-users Digest, Vol 159, Issue 125
> *******************************************************
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