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Cannot Open File Topol.tpr

Topology file -o topol.tprOutput Run input file: tpr tpb tpa -t traj.trrInput, Opt.Full precision trajectory: trr trj cpt -e ener.edrInput, Opt.Energy file: edr ene How to react? Read http://www.gromacs.org/mailing_lists/users.php[UTF-8?]???????????????????????????????????????????????????????????????????????????????????????????????????????????????? [UTF-8?]????????????????????_________________________________________________________________ Express yourself instantly with MSNMessenger! 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 have a peek at this web-site

Count trailing truths Adverb for "syntax" Can I hint the optimizer by giving the range of an integer? LemkulGraduate Research AssistantDepartment of BiochemistryVirginia TechBlacksburg, VAjalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin========================================------------------------------Message: 6Date: Mon, 02 Mar 2009 04:59:51 +1100From: Mark Abraham Subject: Re: [gmx-users] QuestionTo: Discussion list for GROMACS users Lemkul)6. Thelength of box increases in the Z-direction and decreases in the X/Y-directionwith time. 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========================================------------------------------Message: 6Date: Mon, 02 Mar 2009 04:59:51 +1100From: Mark Abraham Subject: Re: [gmx-users] QuestionTo: Discussion list for GROMACS users

I prepared it with: grompp -f cutoff.mdp -c conf.gro -p topol.top -np 2 (here i had to read the archives to avoid temptation to include -nt 2, which even including --enable-threads This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by Use thewww interface or send it to gmx-users-request at gromacs.org.Can't post? It must be only em.tpr, right?

Read http://www.gromacs.org/mailing_lists/users.php???????????????????????????????????????????????????????? ??????????_________________________________________________________________Express yourself instantly with MSN Messenger! gle-phasesystem,i.e., pure water, the Parrinello-Rahman P-coupling can indeedproducethe expected pressure with the deviation less than 2 bar. Perhaps 500 ps is too short of a timeframe to arrive atthe average.Heterogeneous systems often take longer to equilibrate.-JustinThanks a lot.Guang-Jun------------------------------------------------------------------------???????? http://comments.gmane.org/gmane.science.biology.gromacs.user/19906 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

Correspondingly, the compressibility and ref_p are givenfor the x/y and z directions with the same original values,respectively. Biophys. In that case alsoalways check whether your line reads exactly the same as is stated inthe tutorial. 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

Re: Question (Mark Abraham)7. https://www.researchgate.net/post/Gromacs_error_mdrun Copyright (c) 1991-2000, University of Groningen, The Netherlands. Black) Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 2 gcq#171: "I'm a Jerk" (F. Read http://www.gromacs.org/mailing_lists/users.php--Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt) Mark Abraham 2009-03-03 20:32:10 UTC PermalinkRaw Message Post by drugdesignOh, I am very sorry, I've copied the wrong error.That's life - but one needs to

Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Christian Wennberg Maarten Wolf and the project leaders: http://sauvblog.com/cannot-open/cannot-open-transaction-log-file-no-such-file-or-directory.html Then you will need to equilibrate that box for a while to get a good mix of solvents at reasonable density and pressure. Lemkul) > 6. Thank you very much !

I am strange to the value and several tests arerun, mentioned previously. It needs to bemdrun -v -deffnm emThere are default file names for all files supplied by options to GROMACSprograms. Wassenaar, Ph.D.Junior UD (post-doc)Biomolecular NMR, Bijvoet CenterUtrecht UniversityPadualaan 83584 CH UtrechtThe NetherlandsP: +31-30-2539931F: +31-30-2537623 4 Replies 39 Views Switch to linear view Disable enhanced parsing Permalink to this page Thread Navigation http://sauvblog.com/cannot-open/cannot-open-include-file-delay-c-no-such-file-or-directory.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! !

Never mind, I found the answer by myself... 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 Lemkul 2009-03-03 12:59:10 UTC J.

If an image is rotated losslessly, why does the file size change?

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 Use thewww interface or send it to gmx-users-request at gromacs.org.Can't post? Then increase the size of the box, and use the -nmol and -ci options to genbox to add enough methanols to make the mix 70/30. I think you should be able to use that box later for subsequently doing genbox for your protein.

That is what you should get and what you indeed do get; x/y getsmaller, z gets larger, decreasing the surface area.If you have a x/y surface, you should keep the x/y Read http://www.gromacs.org/mailing_lists/users.php------------------------------------------------------------------------???????????????????????????????????????????????????????? ??????????------------------------------------------------------------------------Express yourself instantly with MSN Messenger! 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. http://sauvblog.com/cannot-open/cannot-open-include-file-cmath-no-such-file-or-directory.html Read http://www.gromacs.org/mailing_lists/users.php >> > -- ======================================== Justin A.

Lemkul jalemkul at vt.edu Tue Mar 3 13:59:10 CET 2009 Previous message: [gmx-users] Can not open file: topol.tpr Next message: [gmx-users] Can not open file: topol.tpr Messages sorted by: [ date Read http://www.gromacs.org/mailing_lists/users.php--========================================Justin A. Forexample, I set ref_p=300 bar in the mdp file but obtain an averagepressure as ~330 bar (over 0.5 ns). Lemkul)6.

I've installed LAM-MPI (7.1.2) and FFTW3 in my two Dual Intel P4 CPU machines (4 physical CPUs, 8 with hyperthreading on, i've already read in the mailing list archive that i tool.top does not found (drugdesign)3. How do i solve it? Read http://www.gromacs.org/mailing_lists/users.php--David van der Spoel, Ph.D., Professor of BiologyMolec.

It needs to bemdrun -v -deffnm emThere are default file names for all files supplied by options toGROMACS programs. Jun 18, 2015 Justin Lemkul · University of Maryland, Baltimore If you issue any GROMACS command without command-line options, the command¬†will look for default file names (conf.gro, topol.tpr, etc.) The error Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch Gerrit Groenhof Christoph Junghans Peter Kasson Carsten Kutzner Per Larsson Justin A. Biol., Uppsala University.Box 596, 75124 Uppsala, Sweden.

by -v deffnm command?From the documentation, it might seem that way. Biophys. Lemkul)4. Re: tool.top does not found (Justin A.

Phone: +46184714205. zhuhongaaa I can say nothing about it! The latter is preferred, but in either case youwill have to manually alter the topology.Post by drugdesignI do not mind edit by hand (I want to learn), I searched in thegmx-users Let me decribes the question in more details.First ,two gaseous mathane systems and one liquid water system areequilibrated at 300 bar and 250 K in advance.