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Cannot Open File Topol.tpr

Re: Question (Mark Abraham) > 7. Thanks again.Guang-JunDate: Sat, 28 Feb 2009 07:43:29 -0500From: jalemkul at vt.eduTo: gmx-users at gromacs.orgSubject: Re: [gmx-users] Cannot obtain the expected pressure usingthe Parrinello-Rahman coupling in a gas-liquid systemIn fact, I once The combined system is performed for3ns with the Parrinello-Rahman barostat, which produces a averagepressure of 327 bar. Use thewww interface or send it to gmx-users-request at gromacs.org.Can't post? http://dekovsoft.com/cannot-open/excel-cannot-open-the-file-because-the-file-format-or-file-extension-is-not-valid-2013.html

Re: Question (Mark Abraham)7. LemkulGraduate Research AssistantDepartment of BiochemistryVirginia TechBlacksburg, VAjalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin========================================------------------------------Message: 4Date: Sun, 1 Mar 2009 11:42:04 -0500From: Miguel Quiliano Meza Subject: [gmx-users] help with FAD topology, pleaseTo: gmx-users at The latter is preferred, but in either case youwill have to manually alter the topology.I do not mind edit by hand (I want to learn), I searched in thegmx-users but no But -deffnm seems to only acton output files, so -s is taking the default, topol.tpr. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040105.html

LemkulGraduate Research AssistantDepartment of BiochemistryVirginia TechBlacksburg, VAjalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin========================================_______________________________________________gmx-users mailing list gmx-users at gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease search the archive at http://www.gromacs.org/search beforeposting!Please don't post (un)subscribe requests to the list. tutorial listed below with amber03 force field, but I get an errorabout tool.top while running grompp with em.mdpWhat can cause such a problem?Best regards,Andrewhttps://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdfandrew at linux-f29d:~/GROMACS_MD/1LYD> grompp -f em.mdp -p tool.top This should provide you with a reasonable starting point forcreating your FAD topology (when you consider that ATP is also part of the forcefield as well).-JustinSo, I would be very grateful

See bugzilla 165. Share a link to this question via email, Google+, Twitter, or Facebook. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. Nikhil Maroli Pondicherry University Gromacs error,mdrun ?

of Cell & Molec. Lemkul" Subject: Re: [gmx-users] tool.top does not foundTo: Discussion list for GROMACS users Message-ID: <49AAA193.4050303 at vt.edu>Content-Type: text/plain; charset=KOI8-R; format=flowedPost by drugdesignDear GROMACS users,I am trying to Read http://www.gromacs.org/mailing_lists/users.php--========================================Justin A. http://comments.gmane.org/gmane.science.biology.gromacs.user/19906 The version of Gromacs I used is 4.0.4.

Use thewww interface or send it to gmx-users-request at gromacs.org.Can't post? I think you should be able to use that box later for subsequently doing genbox for your protein. How to react? MSN [UTF-8?]???????????????????? [UTF-8?]????????????????????????Post by drugdesignPost by drugdesign------------------------------------------------------------------------_______________________________________________! ! ; gmx-users mailing list gmx-users at gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease search the archive at http://www.gromacs.org/search beforeposting!Please don't post (un)subscribe requests to the list.

Just to test the parallel processing, i downloaded and tried to run one of the benchmark tests (d.lzm). Draw a hollow square of # with given width Why did the best potions master have greasy hair? Use thewww interface or send it to gmx-users-request at gromacs.org.Can't post? Download today it's FREE!http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/-------------- next part --------------An HTML attachment was scrubbed...URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090301/c7ec66f3/attachment.html------------------------------_______________________________________________gmx-users mailing listgmx-users at gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease search the archive at http://www.gromacs.org/search before posting!End of gmx-users Digest, Vol 59, Issue 4****************************************-------- ??????????

MSN [UTF-8?]???????????????????????? http://dekovsoft.com/cannot-open/error-in-file-file-ifelse-append-a-w-cannot-open-the-connection.html Question (Elias santos)2. Got a question you need answered quickly? Whatis thematter in the two-phase system?When I've used the Parrinello-Rahman barostat for membrane systems,it worksjust fine.

tool.top does not found (drugdesign)3. The temperature is well controlledby usingeither the Berendsen or the Nose-Hoover T-couplings. If the pressure is rightfor wateralone, then the problem likely comes from the inclusion of your gasphase andwhatever parameters you're using for whatever species you have inthis phase.Examine your parameters and Check This Out There were some changesmade tothe Parrinello-Rahman barostat between 3.3.x and 4.0.x.-JustinGuang-JunDate: Sat, 28 Feb 2009 07:19:30 -0500From: jalemkul at vt.eduTo: gmx-users at gromacs.orgSubject: Re: [gmx-users] Cannot obtain the expected pressure usingthe

I would recommend explicit naming of files and proper use of command-line options. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== Previous message: [gmx-users] Can not open file: topol.tpr Next message: [gmx-users] If your process did not finish in error, be sure to include a "return 0" or "exit(0)" in your C code before exiting the application.

Lemkul" Subject: Re: [gmx-users] help with FAD topology, pleaseTo: Discussion list for GROMACS users Message-ID: <49AABD7A.2030300 at vt.edu>Content-Type: text/plain; charset=ISO-8859-1; format=flowedDear all.I am a new user of

Forexample, I set ref_p=300 bar in the mdp file but obtain an averagepressure as ~330 bar (over 0.5 ns). LemkulGraduate Research AssistantDepartment of BiochemistryVirginia TechBlacksburg, VAjalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin========================================_______________________________________________gmx-users mailing list gmx-users at gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease! ! Count trailing truths Adverb for "syntax" Can I hint the optimizer by giving the range of an integer? Lemkul" Subject: Re: [gmx-users] help with FAD topology, pleaseTo: Discussion list for GROMACS users Message-ID: <49AABD7A.2030300 at vt.edu>Content-Type: text/plain; charset=ISO-8859-1; format=flowedPost by drugdesignDear all.I am a new

If your process did not finish in error, be sure to include a "return 0" or "exit(0)" in your C code before exiting the application. Sign up today to join our community of over 11+ million scientific professionals. I can't figure outwhy I need topol.tpr for energy minimization? http://dekovsoft.com/cannot-open/vmware-unable-to-open-file-vmdk-the-system-cannot-find-the-file-specified.html Harvey) >> >> >> >> _______________________________________________ >> gmx-users mailing list gmx-users at gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to

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