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Date: Thu, 24 Apr 2008 08:22:48 To:<[email protected]> Subject: gmx-users Digest, Vol 48, Issue 82 Send gmx-users mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users <http://www.gromacs.org/mailman/listinfo/gmx-users> or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. AFMM parameter refinement (Abu Naser) 2. Re: position restraints (chandrabhan seniya) ---------------------------------------------------------------------- Message: 1 Date: Thu, 24 Apr 2008 12:15:36 +0000 From: Abu Naser <[EMAIL PROTECTED]> Subject: [gmx-users] AFMM parameter refinement To: <[email protected]> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hi All, Has any body tried doing parameter refinement using Vaiana's python code called afmm.py? A.C. Vaiana, Z. Cournia, I.B. Costescu and J.C. Smith, "AFMM: A molecular mechanics force field vibrational parametrization program'", Computer Physics Communications, 167 (2005), pp.34-42. I have done a test run using propene setup that came along with the code and came across a problem. It gives me the same minimum and current sigma value in every steps as: Minimum sigma: 5782.258565, current sigma: 5782.258565 Dose anybody know what might be the problem? With regards, Abu _________________________________________________________________ Be a superhero and win! Play the Iron Man Mashup Game http://www.ironmanmashup.co.uk <http://www.ironmanmashup.co.uk> ------------------------------ Message: 2 Date: Thu, 24 Apr 2008 17:52:09 +0530 From: "chandrabhan seniya" <[EMAIL PROTECTED]> Subject: Re: [gmx-users] position restraints To: "Discussion list for GROMACS users" <[email protected]> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="utf-8" what is yr real prob tell me? On Thu, Apr 24, 2008 at 5:49 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > Quoting chandrabhan seniya <[EMAIL PROTECTED]>: > > > no prob you wait for some time it will write topology file and the > proceed > > further.. > > I think that a lipid molecule trying to tear itself apart at step 0 would > fall > under the category of a "problem," and it will not disappear on it's own > if we > conveniently ignore it... > > > > > On Thu, Apr 24, 2008 at 5:04 PM, <[EMAIL PROTECTED]> wrote: > > > > > Hi, > > > > > > The full mdrun output when the simulation blows up is: > > > > > > Step 0, time 0 (ps) LINCS WARNING > > > relative constraint deviation after LINCS: > > > max inf (between atoms 6 and 7) rms inf > > > bonds that rotated more than 30 degrees: > > > . > > > . > > > . > > > Warning: 1-4 interaction between 1 and 6 at distance > > > 324490777485109120.000 which is larger than the 1-4 table size 1.000 > nm > > > These are ignored for the rest of the simulation > > > This usually means your system is exploding, > > > if not, you should increase table-extension in your mdp file > > > > > > Thanks Gadi > > > > > > Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>: > > > > > > > > > > Did your minimization converge to a nice, negative potential energy? > > > > Also, what > > > > is the full mdrun output when the simulation blows up? You've > quoted > > > > the last > > > > bit, but it would be more informative to see the whole output, or at > > > > least a > > > > description of it (i.e., LINCS warnings). > > > > > > > > -Justin > > > > > > > > Quoting [EMAIL PROTECTED]: > > > > > > > > > > > > > Hi, > > > > > > > > > > I tried using no temperature coupling and no constraints, that did > not > > > > > help. > > > > > If I run the simulation without the position restraints it works > OK. > > > > > Could there by something wrong with the posre file (I'll attach it > at > > > > > the end of the email). > > > > > I want one of the atoms in the lipid to stay in one place and the > rest > > > > > to wiggle around it. Is there any other way to do that which is > not > > > > > position restraints. > > > > > > > > > > Thanks Gadi > > > > > > > > > > > > > > > [ position_restraints ] > > > > > ; atom type fx fy fz > > > > > 1 1 0 0 0 > > > > > 2 1 0 0 0 > > > > > 3 1 0 0 0 > > > > > 4 1 0 0 0 > > > > > 5 1 0 0 0 > > > > > 6 1 0 0 0 > > > > > 7 1 0 0 0 > > > > > 8 1 1000.0 1000.0 1000.0 > > > > > 9 1 0 0 0 > > > > > 10 1 0 0 0 > > > > > 11 1 0 0 0 > > > > > 12 1 0 0 0 > > > > > 13 1 0 0 0 > > > > > 14 1 0 0 0 > > > > > 15 1 0 0 0 > > > > > 16 1 0 0 0 > > > > > 17 1 0 0 0 > > > > > 18 1 0 0 0 > > > > > 19 1 0 0 0 > > > > > 20 1 0 0 0 > > > > > 21 1 0 0 0 > > > > > 22 1 0 0 0 > > > > > 23 1 0 0 0 > > > > > 24 1 0 0 0 > > > > > 25 1 0 0 0 > > > > > 26 1 0 0 0 > > > > > 27 1 0 0 0 > > > > > 28 1 0 0 0 > > > > > 29 1 0 0 0 > > > > > 30 1 0 0 0 > > > > > 31 1 0 0 0 > > > > > 32 1 0 0 0 > > > > > 33 1 0 0 0 > > > > > 34 1 0 0 0 > > > > > 35 1 0 0 0 > > > > > 36 1 0 0 0 > > > > > 37 1 0 0 0 > > > > > 38 1 0 0 0 > > > > > 39 1 0 0 0 > > > > > 40 1 0 0 0 > > > > > 41 1 0 0 0 > > > > > 42 1 0 0 0 > > > > > 43 1 0 0 0 > > > > > 44 1 0 0 0 > > > > > 45 1 0 0 0 > > > > > 46 1 0 0 0 > > > > > 47 1 0 0 0 > > > > > 48 1 0 0 0 > > > > > 49 1 0 0 0 > > > > > 50 1 0 0 0 > > > > > > > > > > Quoting Mark Abraham <[EMAIL PROTECTED]>: > > > > > > > > > > > [EMAIL PROTECTED] wrote: > > > > > > > > > > > > Please generate replies to the mailing list sensibly. It's very > hard > > > > > to > > > > > > work out who you are quoting where in this email. It'd be easy > just > > > > > to > > > > > > ignore it, and that's the last thing you should want. > > > > > > > > > > > >> Hello, > > > > > >> > > > > > >> I'm trying to run a simulation with one lipid molecule in a > fixed > > > > > >> simulation box without pbc. > > > > > >> I set position restraints on one of the atoms and I seem to > keep on > > > > > >> getting the following error: > > > > > > > > > > > > Why do you want MD of a single lipid and a position restraint on > one > > > > > > atom? If you just want to see a lipid wiggle around, then don't > > > > > create > > > > > > more numerical complexity. > > > > > > > > > > > >> The lipid is DPPC.The .itp file I got from a coworker that used > it > > > > > >> before for membrane MD simulations. > > > > > >> To minimize the system I used steepest descent with the > following > > > > > >> parameters: > > > > > > > > > > > > Well if your grompp and mdrun completed successfully and without > > > > > > warnings then you've probably got an OK topology and structure. > > > > > > > > > > > > The combination of all bond constraints, a single lipid in > vacuo, > > > > > > temperature coupling and a single position restraint sounds like > a > > > > > > recipe for a numerical disaster, i.e. blowing up. Try with fewer > of > > > > > > those things applied, or get a more physically-reasonable > system, > > > > > like > > > > > > a whole membrane. > > > > > > > > > > > > Mark > > > > > > _______________________________________________ > > > > > > gmx-users mailing list [email protected] > > > > > > http://www.gromacs.org/mailman/listinfo/gmx-users <http://www.gromacs.org/mailman/listinfo/gmx-users> > > > > > > Please search the archive at http://www.gromacs.org/searchbefore <http://www.gromacs.org/searchbefore> > > > > > posting! > > > > > > Please don't post (un)subscribe requests to the list. Use the > www > > > > > > interface or send it to [EMAIL PROTECTED] > > > > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php <http://www.gromacs.org/mailing_lists/users.php> > > > > > > > > > > > > > > > > > > > > ---------------------------------------------------------------- > > > > > This message was sent using IMP, the Internet Messaging Program. > > > > > > > > > > _______________________________________________ > > > > > gmx-users mailing list [email protected] > > > > > http://www.gromacs.org/mailman/listinfo/gmx-users <http://www.gromacs.org/mailman/listinfo/gmx-users> > > > > > Please search the archive at http://www.gromacs.org/search <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 [EMAIL PROTECTED] > > > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php <http://www.gromacs.org/mailing_lists/users.php> > > > > > > > > > > > > > > > > > > > > > > ======================================== > > > > > > > > Justin A. Lemkul > > > > Graduate Research Assistant > > > > Department of Biochemistry > > > > Virginia Tech > > > > Blacksburg, VA > > > > [EMAIL PROTECTED] | (540) 231-9080 > > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/> > > > > > > > > ======================================== > > > >_______________________________________________ > > > > gmx-users mailing list [email protected] > > > > http://www.gromacs.org/mailman/listinfo/gmx-users <http://www.gromacs.org/mailman/listinfo/gmx-users> > > > > Please search the archive at http://www.gromacs.org/search <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 [EMAIL PROTECTED] > > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php <http://www.gromacs.org/mailing_lists/users.php> > > > > > > > > > > > > > > > > > ---------------------------------------------------------------- > > > This message was sent using IMP, the Internet Messaging Program. > > > > > >_______________________________________________ > > > gmx-users mailing list [email protected] > > > http://www.gromacs.org/mailman/listinfo/gmx-users <http://www.gromacs.org/mailman/listinfo/gmx-users> > > > Please search the archive at http://www.gromacs.org/search <http://www.gromacs.org/search> before > posting! > > > Please don't post (un)subscribe requests to the list. Use thewww > interface > > > or send it to [EMAIL PROTECTED] > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php <http://www.gromacs.org/mailing_lists/users.php> > > > > > > > > > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/> > > ======================================== >_______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users <http://www.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/search <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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php <http://www.gromacs.org/mailing_lists/users.php> > -------------- next part -------------- An HTML attachment was scrubbed... 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