It's not mdrun -v deffnm em, but: mdrun -v -deffnm em Rui
On Tue, 03 Mar 2009 15:52:36 +0300, drugdesign wrote > Oh, I am very sorry, I've copied the wrong error. Actually error was with the > same tutorial at the next step with mdrun -v deffnm em. I can't figure out > why I need topol.tpr for energy minimization? It must be only em.tpr, right? > by -v deffnm command? > > ------------------------------------------------------- > Program mdrun, VERSION 4.0.2 > Source code file: gmxfio.c, line: 736 > > Can not open file: > topol.tpr > ------------------------------------------------------- > > "I Smell Smoke From a Gun Named Extinction" (Pixies) > > and...@linux-f29d:~/GROMACS_MD/1LYD> mdrun -v deffnm em > > -------- [UTF-8?]ÐеÑеÑÑлаемое [UTF-8?]ÑообÑение -------- > 02.03.09, 00:19, gmx-users-requ...@gromacs.org: > > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > Today's Topics: > > 1. Question (Elias santos) > 2. tool.top does not found (drugdesign) > 3. Re: tool.top does not found (Justin A. Lemkul) > 4. help with FAD topology, please (Miguel Quiliano Meza) > 5. Re: help with FAD topology, please (Justin A. Lemkul) > 6. Re: Question (Mark Abraham) > 7. RE: Cannot obtain the expected pressure using the > Parrinello-Rahman coupling in a gas-liquid system (Berk Hess) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 1 Mar 2009 09:14:36 -0300 > From: Elias santos <silvasantoss...@gmail.com> > Subject: [gmx-users] Question > To: gmx-users-request <gmx-users-requ...@gromacs.org>, gmx-users > <gmx-users@gromacs.org> > Message-ID: > <97baf6380903010414v50f35a14l47d66fbf020a2...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi!! > > I am changing my equipment for a AMD quad Core with two physical > processors and would like to know if in this configuration I will have > problems of compatibility with gromacs 4.0. > > Elias Silva > > ------------------------------ > > Message: 2 > Date: Sun, 01 Mar 2009 17:07:25 +0300 > From: drugdesign <drugdes...@yandex.ru> > Subject: [gmx-users] tool.top does not found > To: gmx-users@gromacs.org > Message-ID: <29071235916...@webmail45.yandex.ru> > Content-Type: text/plain; charset=KOI8-R > > Dear GROMACS users, > I am trying to perform [UTF-8?]thе tutorial listed below with amber03 force > field, > but I get an error about tool.top while running grompp with em.mdp What can > cause such a problem? Best regards, Andrew > > https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf > > This is a command line: > > and...@linux-f29d:~/GROMACS_MD/1LYD> grompp -f em.mdp -p tool.top -c > solvated.gro -o em.tpr > > checking input for internal consistency... > > ------------------------------------------------------- > Program grompp, VERSION 4.0.2 > Source code file: grompp.c, line: 810 > > Fatal error: > tool.top does not exist > ------------------------------------------------------- > > "Baseball Heroes Only" (P.J. Harvey) > > ------------------------------ > > Message: 3 > Date: Sun, 01 Mar 2009 09:54:11 -0500 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] tool.top does not found > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <49aaa193.4050...@vt.edu> > Content-Type: text/plain; charset=KOI8-R; format=flowed > > drugdesign wrote: > > Dear GROMACS users, > > I am trying to perform [UTF-8?]thе tutorial listed below with amber03 > > force field, but I get an error > > about tool.top while running grompp with em.mdp > > What can cause such a problem? > > Best regards, > > Andrew > > > > https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf > > > > This is a command line: > > > > and...@linux-f29d:~/GROMACS_MD/1LYD> grompp -f em.mdp -p tool.top -c > > solvated.gro -o em.tpr > > > > checking input for internal consistency... > > > > ------------------------------------------------------- > > Program grompp, VERSION 4.0.2 > > Source code file: grompp.c, line: 810 > > > > Fatal error: > > tool.top does not exist > > ------------------------------------------------------- > > > > tool.top != topol.top; watch for typos! > > -Justin > > > "Baseball Heroes Only" (P.J. Harvey) > > > > > > > > _______________________________________________ > > gmx-users mailing list gmx-users@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 the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > ------------------------------ > > Message: 4 > Date: Sun, 1 Mar 2009 11:42:04 -0500 > From: Miguel Quiliano Meza <rifaxim...@gmail.com> > Subject: [gmx-users] help with FAD topology, please > To: gmx-users@gromacs.org > Message-ID: > <6c2f55e30903010842g462991c8nf4fe6189dfb34...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all. > > I am a new user of GROMACS, I have read the user book and free tutorials in > the WEB, but now when I try to do a simulation, appears FAD no topology, I > have been reading that PRODRG server is a way to achieve that goal, I tried > but the output format is different, it means old version (for gromos 96 > forcefield). > > I do not mind edit by hand (I want to learn), I searched in the gmx-users > but no one shares the FAD topology. Until now, I can't run my simulation. > > So, I would be very grateful if someone could give me "tips", advices or the > FAD topology (in this way I could see my errors). > > Thanks in advance. > > Miguel. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.gromacs.org/pipermail/gmx- > users/attachments/20090301/f949f50e/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Sun, 01 Mar 2009 11:53:14 -0500 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] help with FAD topology, please > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <49aabd7a.2030...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Miguel Quiliano Meza wrote: > > Dear all. > > > > I am a new user of GROMACS, I have read the user book and free tutorials > > in the WEB, but now when I try to do a simulation, appears FAD no > > topology, I have been reading that PRODRG server is a way to achieve > > that goal, I tried but the output format is different, it means old > > version (for gromos 96 forcefield). > > > > PRODRG will give ffgmx-compatible output, but PRODRG beta will give > Gromos96-compatible output. The latter is preferred, but in either case you > will have to manually alter the topology. > > > I do not mind edit by hand (I want to learn), I searched in the > > gmx-users but no one shares the FAD topology. Until now, I can't run my > > simulation. > > > > In the .rtp file of several Gromos96 force fields you will find a few > different FMN variants. This should provide you with a reasonable starting > point for creating your FAD topology (when you consider that ATP is also part > of the force field as well). > > -Justin > > > So, I would be very grateful if someone could give me "tips", advices or > > the FAD topology (in this way I could see my errors). > > > > Thanks in advance. > > > > Miguel. > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list gmx-users@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 the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > ------------------------------ > > Message: 6 > Date: Mon, 02 Mar 2009 04:59:51 +1100 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] Question > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <49aacd17.20...@anu.edu.au> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Elias santos wrote: > > Hi!! > > > > I am changing my equipment for a AMD quad Core with two physical > > processors and would like to know if in this configuration I will have > > problems of compatibility with gromacs 4.0. > > No - MPI will be needed, but that is a non-issue. > > Mark > > ------------------------------ > > Message: 7 > Date: Sun, 1 Mar 2009 22:18:51 +0100 > From: Berk Hess <g...@hotmail.com> > Subject: RE: [gmx-users] Cannot obtain the expected pressure using the > Parrinello-Rahman coupling in a gas-liquid system > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <blu134-w328eb76ccb30d2d512d8f08e...@phx.gbl> > Content-Type: text/plain; charset="gb2312" > > Hi, > > But this has nothing to do with bug 165, does it? > > If you have a surface, you have surface tension which tries to minimize the > surface area. That is what you should get and what you indeed do get; x/y get > smaller, z gets larger, decreasing the surface area. > > If you have a x/y surface, you should keep the x/y sizes constant and only > couple z. > > Berk > > From: gu...@hotmail.com > To: gmx-users@gromacs.org > Subject: RE: [gmx-users] Cannot obtain the expected pressure using the > Parrinello-Rahman coupling in a gas-liquid system > Date: Sun, 1 Mar 2009 05:09:39 +0000 > > Hi, > > After I recheck the box, it is indeed the case described in bugzilla 165. The > length of box increases in the Z-direction and decreases in the X/Y-direction > with time. When I prolong the run, it exits abnormally at the time when the > Box-X/Y reduces to a value less than 2*rvdw. When I fix the Box-Z by setting > the compressibility as zero, the semiisotropic with P-R barostat produces the > inaccurate pressure again. Now, I have to use the Berendsen barostat for my > methane-water interface system. > > Guang-Jun > > > Date: Sat, 28 Feb 2009 19:53:10 +0100 > > From: sp...@xray.bmc.uu.se > > To: gmx-users@gromacs.org > > Subject: Re: [gmx-users] Cannot obtain the expected pressure using the > > Parrinello-Rahman coupling in a gas-liquid system > > > > GuoGuangjun wrote: > > > Hi, > > > > > > > > > The question is resolved by changing the pcoupltype from isotropic to > > > semiisotropic. Correspondingly, the compressibility and ref_p are given > > > for the x/y and z directions with the same original values, > > > respectively. The test system includes 300 methane, 1725 water, and 300 > > > methane, forming two interfaces parallel to the xy-plane. Now, the > > > accurate average-total-pressure is obtained from a short run (0.2 ns) > > > with the default tau_p (1 ps). > > > > Please be careful when you use this kind of pressure coupling, you may > > get the right pressure but you box might keep growing in one direction > > forever. See bugzilla 165. Actually I'm pretty sure it will. > > Unfortunately we don't really understand what is going on here. > > > > > > > > > > > > Thank you for your kind replies and useful clues. > > > > > > Guang-Jun > > > > > > ------------------------------------------------------------------------ > > > From: g...@hotmail.com > > > To: gmx-users@gromacs.org > > > Subject: RE: [gmx-users] Cannot obtain the expected pressure using the > > > Parrinello-Rahman coupling in a gas-liquid system > > > Date: Sat, 28 Feb 2009 15:00:50 +0100 > > > > > > Hi, > > > > > > Is 327 bar the averge total pressure or one the of components of the > > > pressure tensor? > > > You will have a surface tension acting in the system causing a > > > difference in the different components. > > > > > > Also it is still not completely clear to me how long you equilibrate and > > > average. > > > Also the results will depend very much on the size of the system. > > > In small systems the pressure fluctuations are enormous. > > > With Berendsen these fluctuations will be surpressed, with PR not. > > > > > > With PR I would use a tau_p of around 10 ps. > > > You might need to average the pressure over several (tens of?) ns (after > > > several ns of equilibration) > > > to obtain a good average. > > > > > > Berk > > > > > > ------------------------------------------------------------------------ > > > From: gu...@hotmail.com > > > To: gmx-users@gromacs.org > > > Subject: RE: [gmx-users] Cannot obtain the expected pressure using the > > > Parrinello-Rahman coupling in a gas-liquid system > > > Date: Sat, 28 Feb 2009 13:51:15 +0000 > > > > > > Hi, Justin, > > > > > > Thanks for your rapid reply. Let me decribes the question in more details. > > > First ,two gaseous mathane systems and one liquid water system are > > > equilibrated at 300 bar and 250 K in advance. Then, the gas systems are > > > put at the both sides of liquid. The combined system is performed for > > > 3ns with the Parrinello-Rahman barostat, which produces a average > > > pressure of 327 bar. I am strange to the value and several tests are > > > run, mentioned previously. All these test runs take the end gro file of > > > the 3ns-run as the beginning. When the berendsen barostat is used, > > > the pressure is OK. When the Parrinello-Rahman barostat is used, the > > > questionary pressure occurs again. Although I will try to make a long > > > run for equilibrium, I think the equilibrium has reached because the > > > ~330 bar is always obtained no matter how long simulations are sampled, > > > from 0.2 ns to 3 ns. The version of Gromacs I used is 4.0.4. By the way, > > > how long did you equilibrate your membrane system and how many atoms > > > in it? Thanks again. > > > > > > Guang-Jun > > > > > > > > > > > > > Date: Sat, 28 Feb 2009 07:43:29 -0500 > > > > From: jalem...@vt.edu > > > > To: gmx-users@gromacs.org > > > > Subject: Re: [gmx-users] Cannot obtain the expected pressure using > > > the Parrinello-Rahman coupling in a gas-liquid system > > > > > > > > > > > > > > > > GuoGuangjun wrote: > > > > > In fact, I once run the gas-liquid interface for 3 ns, the pressure is > > > > > still as high as 327 bar. > > > > > > > > There are two possibilities in my mind: > > > > > > > > 1. 3 ns is still not long enough. > > > > 2. Your gas phase is causing the problem. If the pressure is right > > > for water > > > > alone, then the problem likely comes from the inclusion of your gas > > > phase and > > > > whatever parameters you're using for whatever species you have in > > > this phase. > > > > Examine your parameters and consider how they were derived and > > > whether or not > > > > they are adequate. > > > > > > > > Also, what version of Gromacs are you using? There were some changes > > > made to > > > > the Parrinello-Rahman barostat between 3.3.x and 4.0.x. > > > > > > > > -Justin > > > > > > > > > Guang-Jun > > > > > > > > > > > > > > > > Date: Sat, 28 Feb 2009 07:19:30 -0500 > > > > > > From: jalem...@vt.edu > > > > > > To: gmx-users@gromacs.org > > > > > > Subject: Re: [gmx-users] Cannot obtain the expected pressure using > > > > > the Parrinello-Rahman coupling in a gas-liquid system > > > > > > > > > > > > > > > > > > > > > > > > GuoGuangjun wrote: > > > > > > > > > > > > > > Hi, All, > > > > > > > I am simulating an interface system composed of methane gas and > > > liquid > > > > > > > water in the NPT ensemble. The temperature is well controlled > > > by using > > > > > > > either the Berendsen or the Nose-Hoover T-couplings. As for > > > pressure, > > > > > > > the Berendsen P-coupling also works well. However, the > > > > > Parrinello-Rahman > > > > > > > P-coupling always produces a higher pressure than the expected. > > > > > > > For > > > > > > > example, I set ref_p=300 bar in the mdp file but obtain an average > > > > > > > pressure as ~330 bar (over 0.5 ns). I test the tau_p in the range > > > > > 0.1 ~ > > > > > > > 10 ps, the case does not change. When I test the sin! ! gle-phase > > > > > system, > > > > > > > i.e., pure water, the Parrinello-Rahman P-coupling can indeed > > > produce > > > > > > > the expected pressure with the deviation less than 2 bar. What > > > is the > > > > > > > matter in the two-phase system? > > > > > > > > > > > > > > > > > > > When I've used the Parrinello-Rahman barostat for membrane systems, > > > > > it works > > > > > > just fine. Perhaps 500 ps is too short of a timeframe to arrive at > > > > > the average. > > > > > > Heterogeneous systems often take longer to equilibrate. > > > > > > > > > > > > -Justin > > > > > > > > > > > > > Thanks a lot. > > > > > > > Guang-Jun > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > [UTF-8?]СÐÐЬЯТди MSN [UTF-8?]ÐÐÐÐÐмÐÐÐÐеЯ MSN > > > > > > > [UTF-8? ]ÐÐШÐЮШÐÐÐÐ [UTF-8?]ЯждкÐÐЯТдиÐÐ > > > > > > > <http://im.live.cn/safe/> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > > > > > > > _______________________________________________ > > > > > > >! ! ; gmx-users mailing list gmx-users@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 the list. 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Lemkul > > > > Graduate Research Assistant > > > > Department of Biochemistry > > > > Virginia Tech > > > > Blacksburg, VA > > > > jalemkul[at]vt.edu | (540) 231-9080 > > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > > > > ======================================== > > > > _______________________________________________ > > > > gmx-users mailing list gmx-users@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 the list. Use the > > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > > Can't post? 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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 list > gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 59, Issue 4 > **************************************** > > -------- [UTF-8?]ÐавеÑÑение [UTF-8?]пеÑеÑÑлаемого > [UTF-8?]ÑооР±ÑÐµÐ½Ð¸Ñ -------- > _______________________________________________ > gmx-users mailing list gmx-users@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 the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt) _______________________________________________ gmx-users mailing list gmx-users@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 the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
