[gmx-users] gromacs.org_gmx-users Digest, Vol 177, Issue 90
Aishwarya Dhar
dhar.aishwarya at gmail.com
Tue Jan 29 11:51:11 CET 2019
Re: Radius of gyration and moment of inertia (Dallas Warren)
Yes of course the ratios are similar. The shapes are similar
But when I measure the distance of the two agrregates in VMD , the length
of the aggregates and the width of the aggregates are more or less of the
same dimensions. Which means that the size of the aggregates are
comparable and there is no difference in size. So the Ix Iy Iz values
should be comparable in both the aggregate and not 4x times different.I
want to know why the the Ix Iy Iz values are 4x times different when the
shape dimensions are similar. The aggregate size is similar.
Thanks in advance
Aishwarya
On Tue, Jan 29, 2019 at 10:45 AM <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: Radius of gyration and moment of inertia (Dallas Warren)
> 2. How to adjust the default protonation states in martini itp
> files? (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=)
> 3. trap invalid opcode (Schulz, Roland)
> 4. About fprintf and debugging (Schulz, Roland)
> 5. Re: How to adjust the default protonation states in martini
> itp files? (Peter Kroon)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 29 Jan 2019 09:11:55 +1100
> From: Dallas Warren <dallas.warren at monash.edu>
> To: GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Radius of gyration and moment of inertia
> Message-ID:
> <CAOv1qzZhgaEkHtDkTv=
> 2yXuMfBDWD27yJWCzBmW8dptLNwpQOw at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-January/123938.html
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On Sat, 26 Jan 2019 at 05:11, Aishwarya Dhar <dhar.aishwarya at gmail.com>
> wrote:
>
> > Hi,
> > I am trying to find the moment of inertia of an aggregate.
> > I have used the command gmx gyrate -f test.gro -s test.gro -p yes -mol
> > yes -o out.xvg
> >
> > For two aggregates the the shape is similar but the values are
> > very different for Ix Iy Iz
> >
> > For an aggregate 1
> > Ix Iy Iz
> > 81538.8 243689 251837
> >
> > For aggregate 2
> > Ix Iy Iz
> > 144172 498275 517148
> > Could you please help me as what could the possible solution?
> >
> >
> >
> > Thanks in advance
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 29 Jan 2019 08:38:14 +0800
> From: "=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=" <272699575 at qq.com>
> To: "=?ISO-8859-1?B?Z3JvbWFjcy5vcmdfZ214LXVzZXJz?="
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] How to adjust the default protonation states in
> martini itp files?
> Message-ID: <tencent_4E110FF82399CF6197C4EB17DCE4A446C605 at qq.com>
> Content-Type: text/plain; charset="ISO-8859-1"
>
> Dear martini friends,
>
>
> By default, the "martinize.py" will
>
>
> 1) for backbone atoms, positively charge the N-terminus (atom type Qd),
> and negatively charge the C-terminus (atom type Qa).
>
>
> 2) for side chain chargeable residues, always positively charge the LYS
> and ARG and negatively charge the ASP and GLU.
>
>
> Now I want to change the protonation states based on a particular pH as
> determined by pdb2pqr server.
>
>
> 1) For backbones, if my N-terminus residue is MET:
> 1 Qd 1 MET BB 1 1.0000 ; C
> 2 C5 1 MET SC1 2 0.0000 ; C
>
>
>
> based on "martini_v2.2P_aminoacids.itp" for MET:
> ;id type resnr residu atom cgnr charge
> 1 P5 1 MET BB 1 0
> 2 C5 1 MET SC1 2 0
>
>
>
> should I change to this?
> 1 P5 1 MET BB 1 0.0000 ; C
> 2 C5 1 MET SC1 2 0.0000 ; C
>
>
>
> 2) For side chains, e.g. GLU
> 362 P5 165 GLU BB 362 0.0000 ; C
> 363 Qa 165 GLU SC1 363 -1.0000 ; C
>
>
>
> if I do not want GLU to be negatively charged,
>
>
> based on "martini_v2.2P_aminoacids.itp" for GLU neutral form:
> ;id type resnr residu atom cgnr charge
> 1 P5 1 GLU0 BB 1 0
> 2 P1 1 GLU0 SC1 2 0
>
>
>
> should I change to this?
> 362 P5 165 GLU0 BB 362 0.0000 ; C
> 363 P1 165 GLU0 SC1 363 0.0000 ; C
>
>
>
> Thank you!
>
>
> Yours sincerely
> Cheng
>
> ------------------------------
>
> Message: 3
> Date: Tue, 29 Jan 2019 03:45:53 +0000
> From: "Schulz, Roland" <roland.schulz at intel.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: [gmx-users] trap invalid opcode
> Message-ID:
> <
> BF759D1B2ACA754496CB1E61835C71EA0918FC13 at ORSMSX109.amr.corp.intel.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> This is usually caused by compiling for a different architecture than you
> are running on. Make sure that the setting for GMX_SIMD is matching what
> the compute node is.
>
> Roland
>
>
> Date: Mon, 28 Jan 2019 14:22:39 +0000 (UTC)
>
> From: Michael Brunsteiner <mbx0009 at yahoo.com<mailto:mbx0009 at yahoo.com>>
>
> To: Gmx Users <gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>>
>
> Subject: [gmx-users] trap invalid opcode
>
> Message-ID: <1633317768.2254503.1548685359517 at mail.yahoo.com<mailto:
> 1633317768.2254503.1548685359517 at mail.yahoo.com>>
>
> Content-Type: text/plain; charset=UTF-8
>
>
>
> Hi
>
>
>
> running a gmx job on a newly set-up debian-buster, with intel i7-3820 CPU,
> and one Nvidia 1060 GTX-6Gb architecture, the job dies without further
> notice, nothing in log file, nor in stdout/stderr ...however in
> /var/syslogi find exactly at the time when gromacs stops this message:
>
>
>
> Jan 26 23:42:39 rcpepc00609 kernel: [319870.261302] traps: gmx[21360] trap
> invalid opcode ip:7f68a6ef9ce5 sp:7f68937fddb0 error:0 in
> libgromacs.so.3.5.0[7f68a6418000+13a4000]
>
> this is gmx-2018.5 on `uname -a`
>
> Linux rcpepc00609 4.19.0-1-amd64 #1 SMP Debian 4.19.12-1 (2018-12-22)
> x86_64 GNU/Linux gromacs was compiled with:
>
> CC=gcc-7 CXX=g++-7 cmake .. -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on nivida
> driver version is 410.78 and cuda toolkit version is 10.0.130
>
>
>
> anybody seen this before or some idea whence this error comes?
>
> thanks!!mic
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 29 Jan 2019 03:43:39 +0000
> From: "Schulz, Roland" <roland.schulz at intel.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: [gmx-users] About fprintf and debugging
> Message-ID:
> <
> BF759D1B2ACA754496CB1E61835C71EA0918FC04 at ORSMSX109.amr.corp.intel.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> You use the debug argument i.e. gmx mdrun -debug 1
>
> Roland
>
>
> Date: Mon, 28 Jan 2019 14:49:05 +0000 (UTC)
>
> From: Mahmood Naderan <nt_mahmood at yahoo.com<mailto:nt_mahmood at yahoo.com>>
>
> To: "gromacs.org_gmx-users"
>
> <gromacs.org_gmx-users at maillist.sys.kth.se<mailto:
> gromacs.org_gmx-users at maillist.sys.kth.se>>, Discussion
> List for
>
> GROMACS Users <gmx-users at gromacs.org<mailto:
> gmx-users at gromacs.org>>
>
> Subject: [gmx-users] About fprintf and debugging
>
> Message-ID: <754074597.2299075.1548686945704 at mail.yahoo.com<mailto:
> 754074597.2299075.1548686945704 at mail.yahoo.com>>
>
> Content-Type: text/plain; charset=UTF-8
>
>
>
> Hi
>
> Where should I set the flag in order to see the fprintf statements like
> ??????? if (debug) ??????? { ??????????? fprintf(debug, "PME: number of
> ranks = %d, rank = %d\n", ??????????????????? cr->nnodes, cr->nodeid);
>
>
>
> Any idea?
>
>
>
> Regards,
>
> Mahmood
>
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 29 Jan 2019 10:44:22 +0100
> From: Peter Kroon <p.c.kroon at rug.nl>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] How to adjust the default protonation states
> in martini itp files?
> Message-ID: <13ab9a8e-af25-0130-579d-44cb48208806 at rug.nl>
> Content-Type: text/plain; charset=utf-8
>
> Hi Zhang,
>
>
> I'm fairly sure GLU0 does what you want, but I'm not 100% sure on the
> terminus. It'll probably do what you want, but I've forwarded your
> question to the group to be sure.
>
>
> Peter
>
> On 29-01-19 01:38, ZHANG Cheng wrote:
> > Dear martini friends,
> >
> >
> > By default, the "martinize.py" will
> >
> >
> > 1) for backbone atoms, positively charge the N-terminus (atom type Qd),
> and negatively charge the C-terminus (atom type Qa).
> >
> >
> > 2) for side chain chargeable residues, always positively charge the LYS
> and ARG and negatively charge the ASP and GLU.
> >
> >
> > Now I want to change the protonation states based on a particular pH as
> determined by pdb2pqr server.
> >
> >
> > 1) For backbones, if my N-terminus residue is MET:
> > 1 Qd 1 MET BB 1 1.0000 ; C
> > 2 C5 1 MET SC1 2 0.0000 ; C
> >
> >
> >
> > based on "martini_v2.2P_aminoacids.itp" for MET:
> > ;id type resnr residu atom cgnr charge
> > 1 P5 1 MET BB 1 0
> > 2 C5 1 MET SC1 2 0
> >
> >
> >
> > should I change to this?
> > 1 P5 1 MET BB 1 0.0000 ; C
> > 2 C5 1 MET SC1 2 0.0000 ; C
> >
> >
> >
> > 2) For side chains, e.g. GLU
> > 362 P5 165 GLU BB 362 0.0000 ; C
> > 363 Qa 165 GLU SC1 363 -1.0000 ; C
> >
> >
> >
> > if I do not want GLU to be negatively charged,
> >
> >
> > based on "martini_v2.2P_aminoacids.itp" for GLU neutral form:
> > ;id type resnr residu atom cgnr charge
> > 1 P5 1 GLU0 BB 1 0
> > 2 P1 1 GLU0 SC1 2 0
> >
> >
> >
> > should I change to this?
> > 362 P5 165 GLU0 BB 362 0.0000 ; C
> > 363 P1 165 GLU0 SC1 363 0.0000 ; C
> >
> >
> >
> > Thank you!
> >
> >
> > Yours sincerely
> > Cheng
>
>
> ------------------------------
>
> --
> 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 177, Issue 90
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