[gmx-users] gromacs.org_gmx-users Digest, Vol 171, Issue 84
Raag Saluja
saluja.raag at gmail.com
Wed Jul 25 06:40:42 CEST 2018
Hi! I gave these commands:
gmx_mpi grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr
time -p mpirun gmx_mpi mdrun -v -deffnm md
I kept md.mdp identical to the one given in the tutorial, except that I
changed the number of steps to 25000000.
I got an error saying that 'topol' was inaccessible. The previous steps had
gone smoothly, though.
Looking forward to your kind help!
Regards,
Raag
On Sun, Jul 22, 2018 at 3:30 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: Time series of the number of atoms with the volume
> (Mark Abraham)
> 2. Re: (no subject) (pbuscemi at q.com)
> 3. Re: topol file inaccessible (Quyen V. Vu)
> 4. Re: Tilt in the Bilayer (atb files)
> 5. tutorial problem (??131 ???)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 21 Jul 2018 19:56:07 +0200
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Cc: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Time series of the number of atoms with the
> volume
> Message-ID:
> <CAMNuMAR-7B696e0E5xqJpruErB4_OMz2u=EGri+aLoTPMf-oog at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> There's quite a few examples in its documentation, do look there for ideas.
> You will need to decide some geometric criterion to define the volume of
> the pore.
>
> Mark
>
> On Sat, Jul 21, 2018, 16:27 Mijiddorj B <b.mijiddorj at gmail.com> wrote:
>
> > Dear GMX users,
> >
> > I would like to make analysis of atom numbers within the certain volume
> > such as pore of channel. If you have any experience, please advise me.
> > How can I use gmx select for this purpose?
> >
> > Best regards,
> > Miji
> > --
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>
> ------------------------------
>
> Message: 2
> Date: Sat, 21 Jul 2018 16:57:46 -0500
> From: pbuscemi at q.com
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] (no subject)
> Message-ID: <24D089EB-46C3-460D-9F55-7737D219CE28 at q.com>
> Content-Type: text/plain; charset=us-ascii
>
> Have you tried the "insert-chemicals-after-md" command ?
>
> PB
>
> > On Jul 11, 2018, at 4:50 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> >
> > Hi,
> >
> > Are you trying to observe something about the transition, or merely the
> > different end points?
> >
> > Mark
> >
> >> On Tue, Jul 10, 2018 at 4:12 PM Soham Sarkar <soham9038 at gmail.com>
> wrote:
> >>
> >> Dear all,
> >> I am planning to do a simulation where after 50ns of simulation I want
> to
> >> add some other chemicals in the system and continue it for another
> 50ns, so
> >> that I can have the effect of that chemicals exclusively before and
> after
> >> adding it to the system.Is it at all possible? If yes please tell me the
> >> protocol/ commands or give me some references where this type of
> simulation
> >> is used. Thanks in advance.
> >> -Soham
> >> --
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> >>
> > --
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>
> ------------------------------
>
> Message: 3
> Date: Sun, 22 Jul 2018 08:56:18 +0700
> From: "Quyen V. Vu" <vuqv.phys at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] topol file inaccessible
> Message-ID:
> <CA+CKAfwAwCNmXH=j3HCssdi4=MNK7ScN16Xa3GmROCK81MhrRg at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> you should provide here more information than that
>
> On Sat, Jul 21, 2018 at 11:42 PM, Ali Ahmed <aa5635737 at gmail.com> wrote:
>
> > hi
> > check your commands from misspelling
> >
> > On Sat, Jul 21, 2018 at 10:08 AM, Raag Saluja <saluja.raag at gmail.com>
> > wrote:
> >
> > > Hi!
> > > I'm simulating a heterodimer. The simulation goes really smoothly till
> > the
> > > MD production step where I get an error saying the topol file is
> > > inaccessible. Can you please help?
> > >
> > > Thank you in advance and regards,
> > > Raag
> > > --
> > > Gromacs Users mailing list
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>
> ------------------------------
>
> Message: 4
> Date: Sun, 22 Jul 2018 10:29:11 +0530
> From: atb files <atbfiles at zoho.com>
> To: "gmx-users" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Tilt in the Bilayer
> Message-ID: <164c05b1328.afe11bbc260588.6272321040920082562 at zoho.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Thank you Justin Yogi Sent using Zoho Mail ---- On Tue, 17 Jul 2018
> 17:42:37 +0530?Justin Lemkul <jalemkul at vt.edu> wrote ---- On 7/17/18 3:10
> AM, atb files wrote: > > > > Dear experts,How can I find the tilt in the
> lipids of the Bilayer with respect to Bilayer normalAny gromacs tool which
> can do this.ThanksYogiSent using Zoho Mail > gmx bundle and gmx gangle can
> both do this. -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
> ================================================== -- Gromacs Users
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> ------------------------------
>
> Message: 5
> Date: Sun, 22 Jul 2018 15:48:47 +0800 (CST)
> From: ??131 ??? <18792742916 at 163.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] tutorial problem
> Message-ID: <66726734.9f6e.164c0f65ac8.Coremail.18792742916 at 163.com>
> Content-Type: text/plain; charset=GBK
>
> dear all
> I am a new user,I was doing this tutorial(http://www.
> mdtutorials.com/gmx/membrane_protein/index.html) it said {To use the
> parameters in lipid.itp, we will have to make some changes to our
> pre-packaged GROMOS96 53A6 force field files (in $GMXLIB/gromos53a6.ff).
> Make a copy of this directory in your working directory called
> "gromos53a6_lipid.ff"},I install gromacs in usr/local/ . ,so this WORKING
> DIRECTORY means in which layer of folder ?is it /usr/local/gromacs/
> share/gromacs/top/ ?then this tutorial said (modify forcefield.doc to
> update the description of the force field parameters in it)?so I should
> modify the forcefield .doc in the new created folder called
> gromos53a6_lipid.ff or the initial folder gromos53a6.ff? I will appreciate
> it if anyone can solve my problem.
>
>
> thank you
>
> ------------------------------
>
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