I cant say I fancy one who wants make money on knowing what on other peoples mind, but that does not mean you are the same! :)
I think this worked out, but what the "bug" may be, that after doing 5 simulations twice, each time the confout.gro is something different from the confout.gro that came out afterwards from using gmx trjconv maybe something irrelated and related to linux command line/rights etc? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "Justin Lemkul" <jalem...@vt.edu> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Thursday, September 7, 2017 3:02:10 PM Subject: Re: [gmx-users] DPOSRES not working On 9/7/17 8:52 AM, Sergio Manzetti wrote: > Hey Justin , you sound like Mark Zuckerberg :) I don't know whether that's good or bad... > Here is the command I used: > > gmx trjconv -f traj -o confout5000.gro -b 10000 -e 10000 -dump 10000 is easier than using -b and -e, FYI. > > and it gives the write gro with DNA in the box as it should be. So then things worked, yes? > This confout.gro is not the same as came out from the GMX run, at the same > moment as the TRJ and XTC came In what way? Why does this lead you to believe that your restraints aren't working? The questions I asked before are more diagnostic of whether or not things are functioning. Dumping a (non-PBC-corrected) frame and looking at another one (PBC corrected, albeit perhaps not in the best way) does not say anything about whether or not the algorithms are working. -Justin > > Sergio Manzetti > > [ http://www.fjordforsk.no/logo_hr2.jpg ] > > [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] > Midtun > 6894 Vangsnes > Norge > Org.nr. 911 659 654 > Tlf: +47 57695621 > [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | > Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | > FAP ] > > > > From: "Justin Lemkul" <jalem...@vt.edu> > To: "gmx-users" <gmx-us...@gromacs.org> > Sent: Thursday, September 7, 2017 2:55:05 PM > Subject: Re: [gmx-users] DPOSRES not working > > On 9/7/17 8:45 AM, Sergio Manzetti wrote: >> It seems that GMX simply didn't write out the correct frame. The confout.gro >> file written out is written at the same time as the trajectories, and for >> some reason, this confout.gro file has nothing to do with the last output >> frame from the sims, when produced by gmx trjconv.. > confout.gro is the final frame, re-wrapped for PBC. So it may "look" > different from the final frame of the trajectory, but it's not. > > Unless you actually provide answers to the questions I asked and any > actual commands you're issuing (e.g. what did you do when you say > "produced by gmx trjconv" for instance?), then there's nothing anyone > here can do to help you. We can't see what you're seeing or interpret > what's in your mind :) > > -Justin > >> >> >> >> >> Sergio Manzetti >> >> [ http://www.fjordforsk.no/logo_hr2.jpg ] >> >> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | >> ] >> Midtun >> 6894 Vangsnes >> Norge >> Org.nr. 911 659 654 >> Tlf: +47 57695621 >> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | >> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | >> FAP ] >> >> >> >> From: "Justin Lemkul" <jalem...@vt.edu> >> To: "gmx-users" <gmx-us...@gromacs.org> >> Sent: Thursday, September 7, 2017 2:28:23 PM >> Subject: Re: [gmx-users] DPOSRES not working >> >> On 9/7/17 5:28 AM, Sergio Manzetti wrote: >>> Hi Johannes, yes, they are there in both cases: >>> >>> ; Include Position restraint file >>> #ifdef POSRES >>> #include "posre_DNA_chain_E.itp" >>> #endif >>> >> Do you have a position restraint energy term written in your .log file, >> and if so, what is its magnitude? Does your DNA start at the middle of >> the box (GROMACS convention) or at the coordinate origin (like other >> software)? If you watch the trajectory evolve, what happens? Does the >> DNA move a lot or does it just bounce back and forth around its original >> position (suggesting your box is simply too small and any time an atom >> crosses a boundary, you get a jump)? >> >> -Justin >> -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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