Re: [gmx-users] zig-zag stacking
On Wed, Aug 1, 2018 at 7:42 AM, Nagasree Garapati < nagasree.garap...@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(O) > 304 276-3674(M) > > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of > gromacs.org_gmx-users-requ...@maillist.sys.kth.se requ...@maillist.sys.kth.se> > Sent: Tuesday, July 31, 2018 8:41 PM > To: gromacs.org_gmx-users@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@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-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@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 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] non-global thermostatting > Message-ID: > 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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > > > -- > > Message: 2 > Date: Tue, 31 Jul 2018 20:34:14 + (UTC) > From: Mahboobeh Eslami > To: Discussion List for GROMACS Users > Subject: [gmx-users] potential energy > Message-ID: <806715418.48695.1533069254...@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 a
Re: [gmx-users] zig-zag stacking
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(O) 304 276-3674(M) From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of gromacs.org_gmx-users-requ...@maillist.sys.kth.se Sent: Tuesday, July 31, 2018 8:41 PM To: gromacs.org_gmx-users@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@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-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@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 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] non-global thermostatting Message-ID: 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 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Message: 2 Date: Tue, 31 Jul 2018 20:34:14 + (UTC) From: Mahboobeh Eslami To: Discussion List for GROMACS Users Subject: [gmx-users] potential energy Message-ID: <806715418.48695.1533069254...@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 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] zig-zag stacking Message-ID: 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.garap...@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 sta
Re: [gmx-users] zig-zag stacking
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 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.garap...@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(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-requ...@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-requ...@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-requ...@gromacs.org.
Re: [gmx-users] zig-zag stacking
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.garap...@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(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-requ...@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-requ...@gromacs.org.
[gmx-users] zig-zag stacking
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(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-requ...@gromacs.org.
