Discussion:
[gmx-users] Invalid Diherdrals
Taeho Kim
2003-03-30 00:46:01 UTC
Permalink
Hi,
I got fatal error " Invalid dihedral type 1000" while doing grompp for PR MD. I built 80 surfactant molecules (using genconf/genbox) and did MD in vacuum(after EM), but when I added tens of same molecules more, I got the problem.

What does it mean? Is it invalid structure of molecules? Or is it related to the distance between two molecules added.

Thank
Taeho
David
2003-03-30 02:15:01 UTC
Permalink
Post by Taeho Kim
Hi,
I got fatal error " Invalid dihedral type 1000" while doing grompp for PR MD. I built 80 surfactant molecules (using genconf/genbox) and did MD in vacuum(after EM), but when I added tens of same molecules more, I got the problem.
What does it mean? Is it invalid structure of molecules? Or is it related to the distance between two molecules added.
probably an error in your topology
to add 80 surfactants
you'd write
[ molecules ]
surf 80
Post by Taeho Kim
Thank
Taeho
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Post by Taeho Kim
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--
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Ester Chiessi
2003-03-31 18:51:00 UTC
Permalink
Dear Gromacs users,

I'm working to calculate MD trajectories for a polymer network in water. I built the topology so that chemical bonds across boundaries are mantained.

At the present I could minimize the system and calculate about 40 ps of dynamics, with timestep 0.5 fs, T 303 K with Berendsed and no pressure coupling and constraining by Shake only X-H bonds.
In the md log file the following message is printed every ten steps:

There were 6 inconsistent shifts. Check your topology

(This warning is related to the 'infinite' connectivity, because it is absent if I remove it from the topology)

Total energy showed I was near to the equilibration when the program suddenly stopped for segmentation fault, without saving coordinates and giving other explanations.

I'd like to know if anyone succesfully performed MD in on similar systems, before giving up my hope!

Thanks, Ester.

--
Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Universita' di Roma "Tor Vergata"
Via della Ricerca Scientifica
00133 Roma (Italy)
http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm
e-mail: ester.chiessi at uniroma2.it
Phone: 39*6*72594462
39*6*72594874
Fax:39*6*72594328
David van der Spoel
2003-03-31 19:07:01 UTC
Permalink
Post by Ester Chiessi
Dear Gromacs users,
I'm working to calculate MD trajectories for a polymer network in water. I built the topology so that chemical bonds across boundaries are mantained.
At the present I could minimize the system and calculate about 40 ps of dynamics, with timestep 0.5 fs, T 303 K with Berendsed and no pressure coupling and constraining by Shake only X-H bonds.
There were 6 inconsistent shifts. Check your topology
(This warning is related to the 'infinite' connectivity, because it is absent if I remove it from the topology)
Total energy showed I was near to the equilibration when the program suddenly stopped for segmentation fault, without saving coordinates and giving other explanations.
I'd like to know if anyone succesfully performed MD in on similar systems, before giving up my hope!
try running again with an environment variable set:
setenv GMXFULLPBC 1
Post by Ester Chiessi
Thanks, Ester.
--
Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Universita' di Roma "Tor Vergata"
Via della Ricerca Scientifica
00133 Roma (Italy)
http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm
e-mail: ester.chiessi at uniroma2.it
Phone: 39*6*72594462
39*6*72594874
Fax:39*6*72594328
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
--
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, Dept. of Cell & Mol. Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Ester Chiessi
2003-03-31 19:44:01 UTC
Permalink
Post by David van der Spoel
Post by Ester Chiessi
Dear Gromacs users,
I'm working to calculate MD trajectories for a polymer network in water. I built the topology so that chemical bonds across boundaries are mantained.
At the present I could minimize the system and calculate about 40 ps of dynamics, with timestep 0.5 fs, T 303 K with Berendsed and no pressure coupling and constraining by Shake only X-H bonds.
There were 6 inconsistent shifts. Check your topology
(This warning is related to the 'infinite' connectivity, because it is absent if I remove it from the topology)
Total energy showed I was near to the equilibration when the program suddenly stopped for segmentation fault, without saving coordinates and giving other explanations.
I'd like to know if anyone succesfully performed MD in on similar systems, before giving up my hope!
setenv GMXFULLPBC 1
I forgot to say I always worked so.
Post by David van der Spoel
Post by Ester Chiessi
Thanks, Ester.
--
Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Universita' di Roma "Tor Vergata"
Via della Ricerca Scientifica
00133 Roma (Italy)
http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm
e-mail: ester.chiessi at uniroma2.it
Phone: 39*6*72594462
39*6*72594874
Fax:39*6*72594328
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
--
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, Dept. of Cell & Mol. Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
--
Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Universita' di Roma "Tor Vergata"
Via della Ricerca Scientifica
00133 Roma (Italy)
http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm
e-mail: ester.chiessi at uniroma2.it
Phone: 39*6*72594462
39*6*72594874
Fax:39*6*72594328

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