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-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 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-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 _______________________________________________ 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
