[gmx-users] zig-zag stacking
Lakshman Ji Verma
lakshmanjivrm at gmail.com
Tue Aug 7 04:13:21 CEST 2018
On Wed, Aug 1, 2018 at 7:42 AM, Nagasree Garapati <
nagasree.garapati at mail.wvu.edu> wrote:
> Thank You Dan and Lakshman
>
>
> I will try using gmx editconf and try to translate and see if I could get
> the arrangement.
>
> I am trying to create a super cell of 7x7x1 size and each unit cell has
> about 276 atoms, so I was trying to find out if there is any other simpler
> utility/program like genconf which can do zigzag stacking for such a big
> super cell.
>
>
> Lakshman
>
> I am not sure if I followed your suggestion, how can we translate only
> one molecule in a box using editconf?
You need to generate index file (make_ndx) with a group contaning the
molecule you want to translate. Then use that index file in editconf step.
thanks!
Lakshman
> With Regards
> Nagasree Garapati
> Research Assistant Professor
> Dept of Chemical and Biomedical Engineering
> West Virginia University
> PO Box 6102
> Morgantown, WV 26506-6102
> 304 293-5028<tel:304%20293-5028>(O)
> 304 276-3674(M)
>
>
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of
> gromacs.org_gmx-users-request at maillist.sys.kth.se <gromacs.org_gmx-users-
> request at maillist.sys.kth.se>
> Sent: Tuesday, July 31, 2018 8:41 PM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: gromacs.org_gmx-users Digest, Vol 172, Issue 1
>
> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users at maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
> gromacs.org_gmx-users-request at maillist.sys.kth.se
>
> You can reach the person managing the list at
> gromacs.org_gmx-users-owner at maillist.sys.kth.se
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
> 1. Re: non-global thermostatting (Justin Lemkul)
> 2. potential energy (Mahboobeh Eslami)
> 3. Re: zig-zag stacking (Dan Gil)
> 4. Re: ndx file with frames (Dan Gil)
> 5. Re: zig-zag stacking (Lakshman Ji Verma)
> 6. Re: non-global thermostatting (Alex)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 31 Jul 2018 16:22:29 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] non-global thermostatting
> Message-ID: <ce4b07ac-3cfa-c90e-b4ad-6007ff9c2c4d at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 7/31/18 4:13 PM, Alex wrote:
> >>
> >> No, as all atoms have to be specified within some group. But you can
> >> disable thermostatting on a given group by setting tau_t = -1.
> >>
> >>
> >> Not sure I understand... I have several groups (say, GRP1, GRP2, etc)
> and
> > the only one I want to be thermostatted is SOL. Does that mean that I
> > should have something like:
> >
> > tc-grps = SOL GRP1 GRP2 ...
> > tau_t = 0.1 -1 -1 ...
> >
> > ?
>
> Yes.
>
> > What happens if instead I happen to have only the original statement?
>
> You'll get a fatal error from grompp.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 31 Jul 2018 20:34:14 +0000 (UTC)
> From: Mahboobeh Eslami <mahboobeh.eslami at yahoo.com>
> To: Discussion List for GROMACS Users <gmx-users at gromacs.org>
> Subject: [gmx-users] potential energy
> Message-ID: <806715418.48695.1533069254542 at mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi all GMX usersI did MD simulation under NPT ensembel. I evaluated
> potential energy during?energy minimization, equilibration, and
> productionMD steps.? The plot of? potential energy?indicates the nice,
> steady convergence of potentialenergy during energy minimization step.?The
> first equilibration phase has been conductedunder an NVT ensemble. The
> temperature of the system quickly has been reachedthe target value (300 K)
> during this step. The potential energy has been alsoincreased quickly and
> then reached to steady state. Is the system?in its minimum potential energy
> in this step??The potential energy has been almost constantduring the
> second equilibration phase and production MD.?These steps performed under
> NPT ensemble. Did MD sinualtion perform?appropriately? please guide
> me.Thanks a lot?
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 31 Jul 2018 19:38:41 -0400
> From: Dan Gil <dan.gil9973 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] zig-zag stacking
> Message-ID:
> <CAHMQ-OZLMtGMzvUCb7QbxYFYuAH9DecrVPF
> B3PE-yQ14w+DWMw at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> I haven't tried it, but I wonder if the gmx editconf utility can be used to
> translate groups of atoms, where the group is defined with an index file
> (make_ndx).
>
> Dan
>
> On Tue, Jul 31, 2018 at 1:21 PM, Nagasree Garapati <
> nagasree.garapati at mail.wvu.edu> wrote:
>
> > Hi All
> >
> >
> > I am trying to look at the pore space availability and property
> > differences between supercells created by stacking unitcells on top of
> each
> > other and by zigzag stacking.
> >
> > In Gromacs genconf can be used to create a super cell by stacking unit
> > cells on top of each other, is there a way to create zig zag stacking?
> >
> >
> > Thank You
> >
> > With Regards
> > Nagasree Garapati
> > Research Assistant Professor
> > Dept of Chemical and Biomedical Engineering
> > West Virginia University
> > PO Box 6102
> > Morgantown, WV 26506-6102
> > 304 293-5028<tel:304%20293-5028>(O)
> > 304 276-3674(M)
> >
> > --
> > 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.
> >
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 31 Jul 2018 19:41:46 -0400
> From: Dan Gil <dan.gil9973 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] ndx file with frames
> Message-ID:
> <CAHMQ-OYfmUhCKyY=vSniBHUz-LGsnjUosC8is=xF_yd+LOZRLA@
> mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> I have used gmx select to create groups of atoms for each time frame - the
> indices of the atoms in each group changed with each step. Then I used this
> output in other gromacs utilities such as gmx rdf.
>
> I haven't used plumed, but from your question I believe gmx select might be
> a good start for you.
>
> Dan
>
> On Mon, Jul 30, 2018 at 9:29 AM, Stefano Guglielmo <
> stefano.guglielmo at unito.it> wrote:
>
> > Dear all,
> >
> > I would like to generate an index file containing frame numbers selected
> > according to a parameter contained in plumed output; I could select the
> > desired frames from the output using any scripting/text manipulating
> tool,
> > but I was wondering which should be the suitable format to be read by,
> > let's say, trjconv.
> > Does anyone have any suggestions?
> >
> > Thanks in advance
> > Stefano
> >
> > --
> > Stefano GUGLIELMO PhD
> > Assistant Professor of Medicinal Chemistry
> > Department of Drug Science and Technology
> > Via P. Giuria 9
> > 10125 Turin, ITALY
> > ph. +39 (0)11 6707178
> > --
> > 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.
> >
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 31 Jul 2018 18:50:10 -0500
> From: Lakshman Ji Verma <lakshmanjivrm at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] zig-zag stacking
> Message-ID:
> <CAH3AB9LC_8Fnj4+em+UQmNVzEF5O7yEt6Rs=qPv6Ybsnc=JH
> fQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Adding on to Dan?s suggestions, you can create a box containing two unit
> cell using editconf (translate one molecule accordingly) and then replicate
> that box using genconf to get required confirmation.
>
> Thanks!
> Lakshman
>
> On Tue, Jul 31, 2018 at 6:39 PM Dan Gil <dan.gil9973 at gmail.com> wrote:
>
> > Hi,
> >
> > I haven't tried it, but I wonder if the gmx editconf utility can be used
> to
> > translate groups of atoms, where the group is defined with an index file
> > (make_ndx).
> >
> > Dan
> >
> > On Tue, Jul 31, 2018 at 1:21 PM, Nagasree Garapati <
> > nagasree.garapati at mail.wvu.edu> wrote:
> >
> > > Hi All
> > >
> > >
> > > I am trying to look at the pore space availability and property
> > > differences between supercells created by stacking unitcells on top of
> > each
> > > other and by zigzag stacking.
> > >
> > > In Gromacs genconf can be used to create a super cell by stacking unit
> > > cells on top of each other, is there a way to create zig zag stacking?
> > >
> > >
> > > Thank You
> > >
> > > With Regards
> > > Nagasree Garapati
> > > Research Assistant Professor
> > > Dept of Chemical and Biomedical Engineering
> > > West Virginia University
> > > PO Box 6102
> > > Morgantown, WV 26506-6102
> > > 304 293-5028<tel:304%20293-5028>(O)
> > > 304 276-3674(M)
> > >
> > > --
> > > 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.
> > >
> > --
> > 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.
> >
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 31 Jul 2018 14:29:34 -0600
> From: Alex <nedomacho at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] non-global thermostatting
> Message-ID:
> <CAMJZ6qGd0WepOSECO0aTgDVOzcjhVoBVr4qL_sEKY43ydmWA-Q at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> >
> >
> >>
> > Yes.
>
>
> Okay then, all running here. Thanks.
>
>
> >
> > What happens if instead I happen to have only the original statement?
> >>
> >
> > You'll get a fatal error from grompp.
> >
> > Ah, the beauty of scripted simulations. I started a batch, in which only
> one mdp file had that modification. Naturally, the script moved on to the
> next one and I assumed that everything was peachy.
>
> This approach to specifically _disabling_ thermostatting in Gromacs (as
> opposed to enabling it) is a revelation to me. Live and learn. Thanks.
>
> Alex
>
>
> ------------------------------
>
> --
> 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.
>
> End of gromacs.org_gmx-users Digest, Vol 172, Issue 1
> *****************************************************
> --
> 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.
>
More information about the gromacs.org_gmx-users
mailing list