Hi Bram, So to echo Justin, it's really better if you use distinct names for the files generated at each step. The -deffnm option to mdrun can be helpful there too. This will help you avoid mistakes like this _and_ will ensure you have all the files available in case you need to check where things went wrong if they do.
Cheers, Tsjerk On Thu, Apr 16, 2009 at 12:37 PM, Hoof, B. van <b.v.h...@tue.nl> wrote: > Yes, indeed. The file topol.tpr was not re-created when I used grompp. In > fact, an error was thrown by grompp stating file input/output error: > minimized.gro > > I am embarrased to say that I had used the command >> grompp -f martini_md1.mdp -c minimized.gro -p martini.top -o membr.tpr >> -maxwarn 10 > instead of >> grompp -f martini_md1.mdp -c minimised.gro -p martini.top -o membr.tpr >> -maxwarn 10 > > Unfortunately, because mdout.mdp was created correctly, I hadn't noticed this > error. > > Thank you everyone for your help! > Bram van Hoof > > -----Original Message----- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On > Behalf Of Tsjerk Wassenaar > Sent: donderdag 16 april 2009 12:11 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Problem with grompp? > > Hi Bram, > > Check the creation times for topol.tpr and minimized.gro. First test > the assumption that the former was created later than the latter. If > it's not, then check the grompp output for errors. Maybe pasting it > here can help. > > Cheers, > > Tsjerk > > On Thu, Apr 16, 2009 at 10:57 AM, Hoof, B. van <b.v.h...@tue.nl> wrote: >> Hi Justin, >> >> Thanks for your answer. I am afraid, however, that the problem is then >> somewhat different. Using >> grompp -f martini_md1.mdp -c minimized.gro -p martini.top -maxwarn 10 >> should have created a new topol.tpr, should it not? It did so in previous >> times at least. >> >> If someone knows where I am going wrong, please let me know. >> >> Kind regards, >> Bram >> >> >> >> -----Original Message----- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Justin A. Lemkul >> Sent: woensdag 15 april 2009 18:12 >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] Problem with grompp? >> >> >> >> Hoof, B. van wrote: >>> Hi everyone, >>> >>> Since I am a new user of Gromacs, this problem is probably rather trivial, >>> but I hope one of you would like to help me nonetheless. I have created a >>> starting structure in a not very optimal situation, which I have then >>> minimized. To continue, I would like to equilibrate the system further >>> using leap-frog MD. To do so, I have used grompp in the following way: >>> grompp -f martini_md1.mdp -c minimized.gro -p martini.top -maxwarn 10 >>> >>> This creates the following mdout.mdp: see attachment >>> >>> Now as far as I can see, using the command `mdrun -v -c md_run.gro' should >>> result in performing a 1,000,000 iteration md simulation of this system. >>> However, when I issue that command, instead what I get is this: >>> :-) G R O M A C S (-: >>> >>> Good ROcking Metal Altar for Chronical Sinners >>> >>> :-) VERSION 4.0.4 (-: >>> >>> >>> [...] >>> >>> :-) mdrun (-: >>> >>> Option Filename Type Description >>> ------------------------------------------------------------ >>> [...] >>> >>> Getting Loaded... >>> Reading file topol.tpr, VERSION 4.0.4 (single precision) >>> Loaded with Money >>> >>> Steepest Descents: >>> Tolerance (Fmax) = 1.00000e+01 >>> Number of steps = 10000 >>> Step= 1, Dmax= 1.0e-02 nm, Epot= 1.23314e+20 Fmax= 2.04950e+19, atom= >>> 11163 >>> Step= 2, Dmax= 1.2e-02 nm, Epot= 5.22616e+17 Fmax= 2.22256e+20, atom= >>> 10863 >>> Step= 3, Dmax= 1.4e-02 nm, Epot= 1.46382e+17 Fmax= 7.52962e+17, atom= >>> 10593 >>> Step= 4, Dmax= 1.7e-02 nm, Epot= 1.21703e+17 Fmax= 3.72098e+16, atom= >>> 10331 >>> Step= 5, Dmax= 2.1e-02 nm, Epot= 2.22862e+16 Fmax= 4.87326e+18, atom= >>> 10857 >>> Step= 6, Dmax= 2.5e-02 nm, Epot= 1.09032e+16 Fmax= 4.39937e+15, atom= >>> 15106 >>> Step= 7, Dmax= 3.0e-02 nm, Epot= 1.81517e+15 Fmax= 6.07049e+14, atom= >>> 15230 >>> Step= 8, Dmax= 3.6e-02 nm, Epot= 2.84750e+14 Fmax= 9.82848e+14, atom= >>> 14675 >>> Step= 9, Dmax= 4.3e-02 nm, Epot= 2.33131e+14 Fmax= 2.39469e+13, atom= >>> 11419 >>> Step= 10, Dmax= 5.2e-02 nm, Epot= 7.23189e+12 Fmax= 2.72305e+14, atom= >>> 14565 >>> Step= 11, Dmax= 6.2e-02 nm, Epot= 3.19510e+12 Fmax= 4.82192e+12, atom= >>> 10638 >>> Step= 13, Dmax= 3.7e-02 nm, Epot= 1.82616e+12 Fmax= 1.11184e+13, atom= >>> 11929 >>> [... etc.....] >>> <<< >>> >>> This is a minimization using the steepest descent algorithm. What am I >>> doing wrong here? >>> >>> Thank you in advance for your kind help! >>> >> >> If you use default names (i.e., topol.tpr for output), you can easily confuse >> yourself and wind up running the wrong input file. The mdout.mdp file you >> posted should correspond to MD; most likely you've just re-run the same .tpr >> file that you used for minimization. >> >> -Justin >> >>> Greetings, >>> Bram van Hoof >>> >>> >>> >>> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> gmx-users mailing list gmx-us...@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 >> 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 >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-us...@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 >> _______________________________________________ >> gmx-users mailing list gmx-us...@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 >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > _______________________________________________ > gmx-users mailing list gmx-us...@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 > _______________________________________________ > gmx-users mailing list gmx-us...@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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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
