[gmx-users] Any way to use GROMACS 4.6.x and 5 together
Bin Liu
fdusuperstring at gmail.com
Wed Aug 6 20:45:38 CEST 2014
Dear Tamas and Mark,
Thank you for your help. Since I am using GROMACS 4.6.x and 5, the default
binary names are different, i.e., g_xxx versus gmx xxx, compiling with
different suffixes are not necessary. It seems Mark's idea is most
fault-proof, though sourcing different .bashrc files one at a time defeats
the my purpose of asking this question. Thank you guys anyway.
Regards,
Bin
2014-08-04 9:52 GMT-04:00 <gromacs.org_gmx-users-request at maillist.sys.kth.se
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> Today's Topics:
>
> 1. Re: Any way to use GROMACS 4.6.x and 5 together (Tamas Karpati)
> 2. Error in inflategro.pl (neha bharti)
> 3. Re: Any way to use GROMACS 4.6.x and 5 together (Mark Abraham)
> 4. Re: Any way to use GROMACS 4.6.x and 5 together (Tamas Karpati)
> 5. Re: Error with tabulated potential and tip4p water model
> (Udaya Dahal)
> 6. Re: Output help (Victor Rosas Garcia)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 4 Aug 2014 13:08:00 +0200
> From: Tamas Karpati <tkarpati at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Any way to use GROMACS 4.6.x and 5 together
> Message-ID:
> <
> CAN5Ox5P7MwbSir+JOs13vUx3pe_4XFKFOKsUtZDC8RMBncXYRA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Bin,
>
> On Sat, Aug 2, 2014 at 12:44 PM, massimo sandal <devicerandom at gmail.com>
> wrote:
> > Compile them with different suffixes? So that you have binaries like
> > mdrun_46 and mdrun_50 ?
>
> Additional tip: if you don't want to rename all the executables
> you may simply create a soft link to one of the install folders,
> then -when need to change- remove it then re-create with the other one.
>
> In detail: I have the following lines in my /home/myname/.bashrc:
>
> export PATH=${PATH}:${HOME}/gromacs_bin/bin
> export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HOME}/gromacs_bin/lib
>
> I have two (in fact more) compiled versions: gromacs-4.6.6_bin and
> gromacs-5.0_bin. When I want to use the 4.6.6 version:
>
> rm -f ~/gromacs_bin
> ln -s ~/gromacs-4.6.6_bin ~/gromacs_bin
>
> Then to switch to the other:
>
> rm -f ~/gromacs_bin
> ln -s ~/gromacs-5.0_bin ~/gromacs_bin
>
> If you're in a unix shell, you need to re-open it for .bashrc to take
> effect.
>
> I assumed you're running GROMACS under some Linux/Unix platform
> but probably the same can be achieved on any other OS.
>
> Hope this helps,
> t
>
> > On 2 Aug 2014 00:32, "Bin Liu" <fdusuperstring at gmail.com> wrote:
> >
> >> Dear everyone,
> >>
> >> I am having trouble with putting GROMACS 4.6.x and 5 together. If I put
> >> these two lines in .bashrc file,
> >>
> >> source /usr/local/gromacs4.6.5/bin/GMXRC
> >> source /usr/local/gromacs5.0/bin/GMXRC
> >>
> >> The second line will undo the work by the first line, i.e., I can use
> only
> >> gmx order of GROMACS 5 (for example), not g_order of GROMACS 4.6.5
> >>
> >> Is there any way to let these two versions work together? Or I should
> just
> >> put both directories in the PATH environment variable? Thanks.
> >>
> >> Cheers,
> >>
> >> Bin
> >> --
> >> 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: 2
> Date: Mon, 4 Aug 2014 17:00:10 +0530
> From: neha bharti <nehabharty123 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Error in inflategro.pl
> Message-ID:
> <
> CAJtVTJCQwhbc_S_npBKgV8Q6y3MFkHuW2U7FOkpY4BPRZpbMAQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hello All
>
> I am trying to perform MD for protein ligand protein complex in popc lipid
> with charmm36 force field and also follow Justin A. Lemkul tutorial.
>
> I generated small molecule topology file from SwissParam which provides
> .pdb file for ligand molecule.
> I don't have .gro file for small molecule thats why I have created all the
> file in .pdb file format.
>
> when I run:
>
> perl inflategro.pl system.pdb 4 POPC 0 system_inflated.gro 5 area.dat
>
> it gives error :
>
> Use of uninitialized value $box_x in multiplication (*) at inflategro.pl
> line 339.
> Use of uninitialized value $box_y in multiplication (*) at inflategro.pl
> line 340.
> Scaling lipids....
> There are 0 lipids...
>
>
> How to work with .pdb file to run inflategro.pl command??
>
> can anyone please help me out how to solve this error.
>
> Thanks in advance
>
> Neha bharti
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 4 Aug 2014 07:39:05 -0400
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Any way to use GROMACS 4.6.x and 5 together
> Message-ID:
> <
> CAMNuMAT2Y+LmC9x6_Ju-ZrU1FwL8Xo5yxCm5gr0J6aKEb4rQLw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Just sourcing the corresponding GMXRC when you want to switch is a quicker
> and easier solution!
>
> Mark
>
>
> On Mon, Aug 4, 2014 at 7:08 AM, Tamas Karpati <tkarpati at gmail.com> wrote:
>
> > Dear Bin,
> >
> > On Sat, Aug 2, 2014 at 12:44 PM, massimo sandal <devicerandom at gmail.com>
> > wrote:
> > > Compile them with different suffixes? So that you have binaries like
> > > mdrun_46 and mdrun_50 ?
> >
> > Additional tip: if you don't want to rename all the executables
> > you may simply create a soft link to one of the install folders,
> > then -when need to change- remove it then re-create with the other one.
> >
> > In detail: I have the following lines in my /home/myname/.bashrc:
> >
> > export PATH=${PATH}:${HOME}/gromacs_bin/bin
> > export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HOME}/gromacs_bin/lib
> >
> > I have two (in fact more) compiled versions: gromacs-4.6.6_bin and
> > gromacs-5.0_bin. When I want to use the 4.6.6 version:
> >
> > rm -f ~/gromacs_bin
> > ln -s ~/gromacs-4.6.6_bin ~/gromacs_bin
> >
> > Then to switch to the other:
> >
> > rm -f ~/gromacs_bin
> > ln -s ~/gromacs-5.0_bin ~/gromacs_bin
> >
> > If you're in a unix shell, you need to re-open it for .bashrc to take
> > effect.
> >
> > I assumed you're running GROMACS under some Linux/Unix platform
> > but probably the same can be achieved on any other OS.
> >
> > Hope this helps,
> > t
> >
> > > On 2 Aug 2014 00:32, "Bin Liu" <fdusuperstring at gmail.com> wrote:
> > >
> > >> Dear everyone,
> > >>
> > >> I am having trouble with putting GROMACS 4.6.x and 5 together. If I
> put
> > >> these two lines in .bashrc file,
> > >>
> > >> source /usr/local/gromacs4.6.5/bin/GMXRC
> > >> source /usr/local/gromacs5.0/bin/GMXRC
> > >>
> > >> The second line will undo the work by the first line, i.e., I can use
> > only
> > >> gmx order of GROMACS 5 (for example), not g_order of GROMACS 4.6.5
> > >>
> > >> Is there any way to let these two versions work together? Or I should
> > just
> > >> put both directories in the PATH environment variable? Thanks.
> > >>
> > >> Cheers,
> > >>
> > >> Bin
> > >> --
> > >> 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.
> > --
> > 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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> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 4 Aug 2014 13:48:36 +0200
> From: Tamas Karpati <tkarpati at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Any way to use GROMACS 4.6.x and 5 together
> Message-ID:
> <
> CAN5Ox5Ntpw7zDowgMz1pWm8JHw_QS4akhhSTCz0w0BuZ3mVV3A at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Mark,
>
> Somehow I felt that I should have read the Manual.... thanks :)
>
> Bin, pelase forget my post.
> t
>
>
> On Mon, Aug 4, 2014 at 1:39 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> > Just sourcing the corresponding GMXRC when you want to switch is a
> quicker
> > and easier solution!
> >
> > Mark
> >
> >
> > On Mon, Aug 4, 2014 at 7:08 AM, Tamas Karpati <tkarpati at gmail.com>
> wrote:
> >
> >> Dear Bin,
> >>
> >> On Sat, Aug 2, 2014 at 12:44 PM, massimo sandal <devicerandom at gmail.com
> >
> >> wrote:
> >> > Compile them with different suffixes? So that you have binaries like
> >> > mdrun_46 and mdrun_50 ?
> >>
> >> Additional tip: if you don't want to rename all the executables
> >> you may simply create a soft link to one of the install folders,
> >> then -when need to change- remove it then re-create with the other one.
> >>
> >> In detail: I have the following lines in my /home/myname/.bashrc:
> >>
> >> export PATH=${PATH}:${HOME}/gromacs_bin/bin
> >> export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HOME}/gromacs_bin/lib
> >>
> >> I have two (in fact more) compiled versions: gromacs-4.6.6_bin and
> >> gromacs-5.0_bin. When I want to use the 4.6.6 version:
> >>
> >> rm -f ~/gromacs_bin
> >> ln -s ~/gromacs-4.6.6_bin ~/gromacs_bin
> >>
> >> Then to switch to the other:
> >>
> >> rm -f ~/gromacs_bin
> >> ln -s ~/gromacs-5.0_bin ~/gromacs_bin
> >>
> >> If you're in a unix shell, you need to re-open it for .bashrc to take
> >> effect.
> >>
> >> I assumed you're running GROMACS under some Linux/Unix platform
> >> but probably the same can be achieved on any other OS.
> >>
> >> Hope this helps,
> >> t
> >>
> >> > On 2 Aug 2014 00:32, "Bin Liu" <fdusuperstring at gmail.com> wrote:
> >> >
> >> >> Dear everyone,
> >> >>
> >> >> I am having trouble with putting GROMACS 4.6.x and 5 together. If I
> put
> >> >> these two lines in .bashrc file,
> >> >>
> >> >> source /usr/local/gromacs4.6.5/bin/GMXRC
> >> >> source /usr/local/gromacs5.0/bin/GMXRC
> >> >>
> >> >> The second line will undo the work by the first line, i.e., I can use
> >> only
> >> >> gmx order of GROMACS 5 (for example), not g_order of GROMACS 4.6.5
> >> >>
> >> >> Is there any way to let these two versions work together? Or I should
> >> just
> >> >> put both directories in the PATH environment variable? Thanks.
> >> >>
> >> >> Cheers,
> >> >>
> >> >> Bin
> >> >> --
> >> >> 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.
> >> --
> >> 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: 5
> Date: Mon, 4 Aug 2014 09:48:23 -0400
> From: Udaya Dahal <dahal.udaya at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Error with tabulated potential and tip4p
> water model
> Message-ID:
> <
> CAG1jmThLHC_HvT98xNQ9a3rH3erQzxoyvKSAKn1+XFszYD7KvA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> It was immediate. But I figured out the way to solve that issue. Looks
> like the starting initial configuration was not so good. A different
> starting structure at least gave me the energy minimization to few steps
> but I kind of really find very hard to have the energy minimized to smaller
> value. The maximum force on the particular atom is around ...+03. Do I
> really have to amend each and every atom step by step(which still doesn't
> solve the problem) or there is any other specific way that we can get
> more/less energy minimized structure. Thank you for your help.
>
>
> On Sun, Aug 3, 2014 at 9:23 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Immediately, or after some EM steps?
> >
> > Mark
> >
> >
> > On Sun, Aug 3, 2014 at 12:56 PM, Udaya Dahal <dahal.udaya at gmail.com>
> > wrote:
> >
> > > I have tabulated potential for all the possible combinations(non
> > bonded).
> > > I am using Tip4p water model for the polymer water interaction. While
> > > running the energy minimization i got the error like below.
> > >
> > > Fatal error:
> > > Settle block crossing node boundaries
> > > constraint between atoms 664, 665, 666)
> > > For more information and tips for troubleshooting, please check the
> > GROMACS
> > > website at http://www.gromacs.org/Documentation/Errors
> > >
> > > Any idea to slove this issue.?
> > >
> > > Thank you,
> > > Udaya.
> > > --
> > > 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.
> >
>
>
>
> --
> Udaya Dahal,
> Graduate Assistant,
> Department of Physics,
> University of Connecticut
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 4 Aug 2014 08:52:29 -0500
> From: Victor Rosas Garcia <rosas.victor at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Output help
> Message-ID:
> <
> CAJota7BRPgjsuKxg5FFb6A25u9nKw1TPsxbAMjt4GPMnPbtNrg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> If you are under Linux, you could use "tail" to get rid of the lines
> you don't want. Check "man tail" for details.
>
> Hope this helps
>
> Victor
>
> 2014-08-03 17:57 GMT-05:00 Marco Rougeth <marco at rougeth.com>:
> > Hello!
> >
> > I using grompp and mdrun and the output text shows too much text, like
> the
> > version, contributors names, copyright and all the options used. How can
> I
> > omit all of them? I tried to redirect the output, but it did not worked.
> >
> > Thank you!
> > --
> > 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
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
>
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