[gmx-users] do_dssp segmentation fault
arun kumar
arunjones.kumar89 at gmail.com
Sat Mar 3 08:21:22 CET 2012
yes other gromacs tools are working properly ...i installed gromacs in
/usr/local/
so i used the command /usr/local/gromacs/bin/./do_dssp -s md.tpr -f md.xtc
-o ss.xpm
and i also set the environment variable as export
DSSP=/usr/local/gromacs/bin/do_dssp
On Sat, Mar 3, 2012 at 12:26 PM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
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> 1. Re: Re: Re: Re: Re: mdrun -multi flag (Mark Abraham) (Justin
> A. Lemkul) (Mark Abraham)
> 2. Anomalous temperature (zhongjin)
> 3. do_dssp segmentation fault (arun kumar)
> 4. Re: do_dssp segmentation fault (Mark Abraham)
> 5. Re: Anomalous temperature (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 03 Mar 2012 09:30:24 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Re: Re: Re: Re: mdrun -multi flag (Mark
> Abraham) (Justin A. Lemkul)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4F514A00.6000605 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 3/03/2012 7:34 AM, bo.shuang wrote:
> > Thank you for help! Is that possible to run REMD on a PC with only one
> > processor?
>
> No. See http://www.gromacs.org/Documentation/How-tos/REMD
>
> Mark
>
> >
> > Bo
> >
> > bo.shuang wrote:
> > > Hi, Mark,
> > >
> > > Thank you for help. It works. But now I have new fatal error:
> > >
> > > Fatal error:
> > > The number of nodes (1) is not a multiple of the number of
> > simulations (2)
> > >
> > > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> > > with errorcode -1.
> > >
> > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> > > You may or may not see output from other processes, depending on
> > > exactly when Open MPI kills them.
> > >
> > >
> > > What does it mean about nodes? Thank you!
> > >
> >
> > Running multiple simulations requires multiple processors. For 2
> > simulations,
> > you need at least 2 processors (one for each simulation). More can be
> > used, but
> > it must be a multiple of the number of simulations, as the error
> > message indicates.
> >
> > -Justin
> >
> >
>
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> ------------------------------
>
> Message: 2
> Date: Sat, 3 Mar 2012 14:08:02 +0800 (CST)
> From: zhongjin <zhongjin1000 at yahoo.com.cn>
> Subject: [gmx-users] Anomalous temperature
> To: gmx-users at gromacs.org
> Message-ID:
> <1330754882.32906.YahooMailClassic at web15608.mail.cnb.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear gmx users,
>
> It seems that I have found a strange temperature value after NVT
> equilibrium for 200 ps. I simulate a CNT with two graphite sheets in water
> box. I do not want to them to deform or change their shaps, So I use a very
> large position restraint (1*10^6) to keep their shaps. The temperature was
> set to 300 K, but after NVT equilibrium, the tempertaure was 330K.
>
> .mdp content
> define = -DPOSRES_CNTGATE -DPOSRES_K -DPOSRES_CL
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> tcoupl = v-rescale
> nsttcouple = -1
> nh-chain-length = 1
> ; Groups to couple separately
> tc-grps = Other Water_and_ions
> ; Time constant (ps) and reference temperature (K)
> tau-t = 0.1 0.1
> ref-t = 300 300
>
> results
> Energy Average Err.Est. RMSD Tot-Drift
>
> -------------------------------------------------------------------------------
> Temperature 331.548 2.6 10.3739 15.0042 (K)
> T-Other 436.927 12 39.4112 67.2519 (K)
> T-Water_and_ions 303.349 0.16 6.07417 1.02328 (K)
>
> the Other, that is CNT and two graphite sheets temperature is very high!!!
>
> Howerver when I freeze them, the temperture is OK
>
> freezegrps = K CL Other
> freezedim = Y Y Y Y Y Y Y Y Y
>
> the results is
>
> Energy Average Err.Est. RMSD Tot-Drift
>
> -------------------------------------------------------------------------------
> Temperature 299.998 0.0034 4.84173 -0.0066645 (K)
> T-Other 0 0 0 0 (K)
> T-Water_and_ions 299.998 0.0034 4.84173 -0.0066645 (K)
>
> So I should freeze them or use a small postion restraint to constaint
> them, in order to get the correct temperture?
>
> Zhongjin He
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> ------------------------------
>
> Message: 3
> Date: Sat, 3 Mar 2012 11:44:17 +0530
> From: arun kumar <arunjones.kumar89 at gmail.com>
> Subject: [gmx-users] do_dssp segmentation fault
> To: gmx-users at gromacs.org
> Message-ID:
> <CAGM9vJ8RqoR_nANb2r_6O0tW5ATwuTPmG+R4dvgFYo7usaGGfw at mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear all,
>
> Iam trying to generate secondary structure plot through do_dssp program,
> but there was an error like "segmentation fault"
>
> Reading file md.tpr, VERSION 4.0.7 (single precision)
> Reading file md.tpr, VERSION 4.0.7 (single precision)
> Segmentation fault (core dumped)
> bash-4.1#
>
> can anybody please say what it means and how to solve it
>
> Regards,
> --
> Arun Kumar Somavarapu
> Project-JRF
> Dr. Prasanna's lab
> TMC, ACTREC
> Navi Mumbai-410210
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> ------------------------------
>
> Message: 4
> Date: Sat, 03 Mar 2012 17:47:16 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] do_dssp segmentation fault
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4F51BE74.3010704 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 3/03/2012 5:14 PM, arun kumar wrote:
> > Dear all,
> >
> > Iam trying to generate secondary structure plot through do_dssp
> > program, but there was an error like "segmentation fault"
> >
> > Reading file md.tpr, VERSION 4.0.7 (single precision)
> > Reading file md.tpr, VERSION 4.0.7 (single precision)
> > Segmentation fault (core dumped)
> > bash-4.1#
> >
> > can anybody please say what it means and how to solve it
>
> No, because there's no diagnostic information. Do other GROMACS tools
> work? Does the DSSP executable work?
>
> Mark
>
>
> ------------------------------
>
> Message: 5
> Date: Sat, 03 Mar 2012 17:56:24 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Anomalous temperature
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4F51C098.8090008 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 3/03/2012 5:08 PM, zhongjin wrote:
> > Dear gmx users,
> > It seems that I have found a strange temperature value after NVT
> > equilibrium for 200 ps. I simulate a CNT with two graphite sheets in
> > water box. I do not want to them to deform or change their shaps, So I
> > use a very large position restraint (1*10^6) to keep their shaps. The
> > temperature was set to 300 K, but after NVT equilibrium, the
> > tempertaure was 330K.
> > .mdp content
> > define = -DPOSRES_CNTGATE -DPOSRES_K -DPOSRES_CL
> > ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> > ; Temperature coupling
> > tcoupl = v-rescale
> > nsttcouple = -1
> > nh-chain-length = 1
> > ; Groups to couple separately
> > tc-grps = Other Water_and_ions
> > ; Time constant (ps) and reference temperature (K)
> > tau-t = 0.1 0.1
> > ref-t = 300 300
> > results
> > Energy Average Err.Est. RMSD Tot-Drift
> >
> -------------------------------------------------------------------------------
> > Temperature 331.548 2.6 10.3739 15.0042 (K)
> > T-Other 436.927 12 39.4112 67.2519 (K)
> > T-Water_and_ions 303.349 0.16 6.07417 1.02328 (K)
> > the Other, that is CNT and two graphite sheets temperature is very
> high!!!
> > Howerver when I freeze them, the temperture is OK
> > freezegrps = K CL Other
> > freezedim = Y Y Y Y Y Y Y Y Y
> > the results is
> >
> > Energy Average Err.Est. RMSD Tot-Drift
> >
> -------------------------------------------------------------------------------
> > Temperature 299.998 0.0034 4.84173 -0.0066645 (K)
> > T-Other 0 0 0 0 (K)
> > T-Water_and_ions 299.998 0.0034 4.84173 -0.0066645 (K)
> > So I should freeze them or use a small postion restraint to constaint
> > them, in order to get the correct temperture?
> >
>
> By introducing position restraints, you cause local heating because
> there is a force whenever the positions deviate. Don't try to measure
> local temperature until the model might make a sensible measurement,
> i.e. after equilibration. That might mean several equilibration phases
> where you relax your position restraints gradually.
>
> The thin nature of the sheet and tube is also somewhat unfavorable for
> the correct function of separate T-coupling groups. See manual 3.4.8,
> particularly final subsection and ref therein.
>
> Mark
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--
Arun Kumar Somavarapu
Project-JRF
Dr. Prasanna's lab
TMC, ACTREC
Navi Mumbai-410210
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