yes other gromacs tools are working properly ...i installed gromacs in /usr/local/<br>so i used the command /usr/local/gromacs/bin/./do_dssp -s md.tpr -f md.xtc -o ss.xpm<br>and i also set the environment variable as export DSSP=/usr/local/gromacs/bin/do_dssp<br>
<br><br><div class="gmail_quote">On Sat, Mar 3, 2012 at 12:26 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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Today's Topics:<br>
<br>
1. Re: Re: Re: Re: Re: mdrun -multi flag (Mark Abraham) (Justin<br>
A. Lemkul) (Mark Abraham)<br>
2. Anomalous temperature (zhongjin)<br>
3. do_dssp segmentation fault (arun kumar)<br>
4. Re: do_dssp segmentation fault (Mark Abraham)<br>
5. Re: Anomalous temperature (Mark Abraham)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Sat, 03 Mar 2012 09:30:24 +1100<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Re: Re: Re: Re: mdrun -multi flag (Mark<br>
Abraham) (Justin A. Lemkul)<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4F514A00.6000605@anu.edu.au">4F514A00.6000605@anu.edu.au</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
On 3/03/2012 7:34 AM, bo.shuang wrote:<br>
> Thank you for help! Is that possible to run REMD on a PC with only one<br>
> processor?<br>
<br>
No. See <a href="http://www.gromacs.org/Documentation/How-tos/REMD" target="_blank">http://www.gromacs.org/Documentation/How-tos/REMD</a><br>
<br>
Mark<br>
<br>
><br>
> Bo<br>
><br>
> bo.shuang wrote:<br>
> > Hi, Mark,<br>
> ><br>
> > Thank you for help. It works. But now I have new fatal error:<br>
> ><br>
> > Fatal error:<br>
> > The number of nodes (1) is not a multiple of the number of<br>
> simulations (2)<br>
> ><br>
> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD<br>
> > with errorcode -1.<br>
> ><br>
> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.<br>
> > You may or may not see output from other processes, depending on<br>
> > exactly when Open MPI kills them.<br>
> ><br>
> ><br>
> > What does it mean about nodes? Thank you!<br>
> ><br>
><br>
> Running multiple simulations requires multiple processors. For 2<br>
> simulations,<br>
> you need at least 2 processors (one for each simulation). More can be<br>
> used, but<br>
> it must be a multiple of the number of simulations, as the error<br>
> message indicates.<br>
><br>
> -Justin<br>
><br>
><br>
<br>
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Message: 2<br>
Date: Sat, 3 Mar 2012 14:08:02 +0800 (CST)<br>
From: zhongjin <<a href="mailto:zhongjin1000@yahoo.com.cn">zhongjin1000@yahoo.com.cn</a>><br>
Subject: [gmx-users] Anomalous temperature<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:1330754882.32906.YahooMailClassic@web15608.mail.cnb.yahoo.com">1330754882.32906.YahooMailClassic@web15608.mail.cnb.yahoo.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear gmx users,<br>
<br>
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.<br>
<br>
.mdp content<br>
define = -DPOSRES_CNTGATE -DPOSRES_K -DPOSRES_CL<br>
; OPTIONS FOR WEAK COUPLING ALGORITHMS<br>
; Temperature coupling <br>
tcoupl = v-rescale<br>
nsttcouple = -1<br>
nh-chain-length = 1<br>
; Groups to couple separately<br>
tc-grps = Other Water_and_ions<br>
; Time constant (ps) and reference temperature (K)<br>
tau-t = 0.1 0.1<br>
ref-t = 300 300<br>
<br>
results<br>
Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>
Temperature 331.548 2.6 10.3739 15.0042 (K)<br>
T-Other 436.927 12 39.4112 67.2519 (K)<br>
T-Water_and_ions 303.349 0.16 6.07417 1.02328 (K)<br>
<br>
the Other, that is CNT and two graphite sheets temperature is very high!!!<br>
<br>
Howerver when I freeze them, the temperture is OK<br>
<br>
freezegrps = K CL Other<br>
freezedim = Y Y Y Y Y Y Y Y Y<br>
<br>
the results is<br>
<br>
Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>
Temperature 299.998 0.0034 4.84173 -0.0066645 (K)<br>
T-Other 0 0 0 0 (K)<br>
T-Water_and_ions 299.998 0.0034 4.84173 -0.0066645 (K)<br>
<br>
So I should freeze them or use a small postion restraint to constaint them, in order to get the correct temperture?<br>
<br>
Zhongjin He<br>
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<br>
Message: 3<br>
Date: Sat, 3 Mar 2012 11:44:17 +0530<br>
From: arun kumar <<a href="mailto:arunjones.kumar89@gmail.com">arunjones.kumar89@gmail.com</a>><br>
Subject: [gmx-users] do_dssp segmentation fault<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:CAGM9vJ8RqoR_nANb2r_6O0tW5ATwuTPmG%2BR4dvgFYo7usaGGfw@mail.gmail.com">CAGM9vJ8RqoR_nANb2r_6O0tW5ATwuTPmG+R4dvgFYo7usaGGfw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear all,<br>
<br>
Iam trying to generate secondary structure plot through do_dssp program,<br>
but there was an error like "segmentation fault"<br>
<br>
Reading file md.tpr, VERSION 4.0.7 (single precision)<br>
Reading file md.tpr, VERSION 4.0.7 (single precision)<br>
Segmentation fault (core dumped)<br>
bash-4.1#<br>
<br>
can anybody please say what it means and how to solve it<br>
<br>
Regards,<br>
--<br>
Arun Kumar Somavarapu<br>
Project-JRF<br>
Dr. Prasanna's lab<br>
TMC, ACTREC<br>
Navi Mumbai-410210<br>
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<br>
Message: 4<br>
Date: Sat, 03 Mar 2012 17:47:16 +1100<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] do_dssp segmentation fault<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4F51BE74.3010704@anu.edu.au">4F51BE74.3010704@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
On 3/03/2012 5:14 PM, arun kumar wrote:<br>
> Dear all,<br>
><br>
> Iam trying to generate secondary structure plot through do_dssp<br>
> program, but there was an error like "segmentation fault"<br>
><br>
> Reading file md.tpr, VERSION 4.0.7 (single precision)<br>
> Reading file md.tpr, VERSION 4.0.7 (single precision)<br>
> Segmentation fault (core dumped)<br>
> bash-4.1#<br>
><br>
> can anybody please say what it means and how to solve it<br>
<br>
No, because there's no diagnostic information. Do other GROMACS tools<br>
work? Does the DSSP executable work?<br>
<br>
Mark<br>
<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Sat, 03 Mar 2012 17:56:24 +1100<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Anomalous temperature<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4F51C098.8090008@anu.edu.au">4F51C098.8090008@anu.edu.au</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
On 3/03/2012 5:08 PM, zhongjin wrote:<br>
> Dear gmx users,<br>
> It seems that I have found a strange temperature value after NVT<br>
> equilibrium for 200 ps. I simulate a CNT with two graphite sheets in<br>
> water box. I do not want to them to deform or change their shaps, So I<br>
> use a very large position restraint (1*10^6) to keep their shaps. The<br>
> temperature was set to 300 K, but after NVT equilibrium, the<br>
> tempertaure was 330K.<br>
> .mdp content<br>
> define = -DPOSRES_CNTGATE -DPOSRES_K -DPOSRES_CL<br>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS<br>
> ; Temperature coupling<br>
> tcoupl = v-rescale<br>
> nsttcouple = -1<br>
> nh-chain-length = 1<br>
> ; Groups to couple separately<br>
> tc-grps = Other Water_and_ions<br>
> ; Time constant (ps) and reference temperature (K)<br>
> tau-t = 0.1 0.1<br>
> ref-t = 300 300<br>
> results<br>
> Energy Average Err.Est. RMSD Tot-Drift<br>
> -------------------------------------------------------------------------------<br>
> Temperature 331.548 2.6 10.3739 15.0042 (K)<br>
> T-Other 436.927 12 39.4112 67.2519 (K)<br>
> T-Water_and_ions 303.349 0.16 6.07417 1.02328 (K)<br>
> the Other, that is CNT and two graphite sheets temperature is very high!!!<br>
> Howerver when I freeze them, the temperture is OK<br>
> freezegrps = K CL Other<br>
> freezedim = Y Y Y Y Y Y Y Y Y<br>
> the results is<br>
><br>
> Energy Average Err.Est. RMSD Tot-Drift<br>
> -------------------------------------------------------------------------------<br>
> Temperature 299.998 0.0034 4.84173 -0.0066645 (K)<br>
> T-Other 0 0 0 0 (K)<br>
> T-Water_and_ions 299.998 0.0034 4.84173 -0.0066645 (K)<br>
> So I should freeze them or use a small postion restraint to constaint<br>
> them, in order to get the correct temperture?<br>
><br>
<br>
By introducing position restraints, you cause local heating because<br>
there is a force whenever the positions deviate. Don't try to measure<br>
local temperature until the model might make a sensible measurement,<br>
i.e. after equilibration. That might mean several equilibration phases<br>
where you relax your position restraints gradually.<br>
<br>
The thin nature of the sheet and tube is also somewhat unfavorable for<br>
the correct function of separate T-coupling groups. See manual 3.4.8,<br>
particularly final subsection and ref therein.<br>
<br>
Mark<br>
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End of gmx-users Digest, Vol 95, Issue 16<br>
*****************************************<br>
</font></span></blockquote></div><br><br clear="all"><br>-- <br>Arun Kumar Somavarapu<br>Project-JRF<br><div>Dr. Prasanna's lab<br>TMC, ACTREC<br>Navi Mumbai-410210<br></div><br>