[gmx-users] zig-zag stacking
Nagasree Garapati
nagasree.garapati at mail.wvu.edu
Wed Aug 1 14:42:25 CEST 2018
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?
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)
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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
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------------------------------
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-OZLMtGMzvUCb7QbxYFYuAH9DecrVPFB3PE-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
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> * Please search the archive at http://www.gromacs.org/
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------------------------------
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 at 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
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>
------------------------------
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=JHfQ 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
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> posting!
>
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------------------------------
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
------------------------------
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