I overlooked that you printed dVdl, not dGdl. Without looking into the code, I would not know where term is missing. Can you figure out if any energy terms are missing in the print? Please check if all energy terms in de log file are present in the dvdl print. I would guess that the dvdl numbers are correct, but there could be a mistake in there as well.
Selectively turning off perturbations would find it, but that is a bit of work. Berk. > It is a single processor simulation. > > As I change some masses,I have indeed a change in Ekin (-1,23e+00) , but it > should not explain what happens with Vpot, should it ? > I also have position restraints whose parameters do not change, so dVdl > should be 0, which is what it reads. I did > not copy this in my previous mail, I should have. > > Thanks for your help, > Michael Bon > > > -------- Message d'origine-------- > De: [EMAIL PROTECTED] de la part de [EMAIL PROTECTED] > Date: mar. 29/01/2008 12:00 > À: [email protected] > Objet : gmx-users Digest, Vol 45, Issue 116 > > 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 > 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. Re: dihedral restraints wiki section (Behnoush Zare) > 2. RE : FEP : separating components of dgdl (BON Michael) > 3. RE: RE : FEP : separating components of dgdl (Berk Hess) > 4. Re: dihedral restraints wiki section (Xavier Periole) > 5. Re: GROMACS ON CYGWIN. (Nabajyoti Goswami) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 29 Jan 2008 13:06:14 +0330 (IRST) > From: Behnoush Zare <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] dihedral restraints wiki section > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=utf-8 > > Dear chris, > > Thank you for your help about performing dihedral restraints. Would you > please kindly explain to me how I can measure the value of dihedral angles > between two amin acids (I mean C'-N-C-C' and N-C-C'-N). > Thank you in advance for your valuable aid. > > Behnoush > > ----- Original Message ----- > From: "chris neale" <[EMAIL PROTECTED]> > To: [email protected] > Sent: Sunday, January 27, 2008 11:49:42 PM (GMT+0330) Asia/Tehran > Subject: [gmx-users] dihedral restraints wiki section > > I have added a section on dihedral restraints to the wiki. > > http://wiki.gromacs.org/index.php/Dihedral_Restraints > > _______________________________________________ > gmx-users mailing list [email protected] > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > ------------------------------ > > Message: 2 > Date: Tue, 29 Jan 2008 10:24:57 +0100 > From: "BON Michael" <[EMAIL PROTECTED]> > Subject: [gmx-users] RE : FEP : separating components of dgdl > To: <[email protected]> > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > > Thanks for the quick reply. > > I have an other question : I ran a quick simulation on a single node using > mdrun -sepdvdl and the components are written in > the .log file. But the final value of dVpot/dlambda doesn't seem to be the > sum of the components above. Example for some step: > > VdW and Coulomb SR : dVdl -2.72859e+02 > Angle : dVdl 3.56537e+00 > Proper Dih. : dVdl -7.31260e-03 > Ryckaert-Bell. : dVdl -1.13654e-01 > LJ-14 + Coulomb-14 : dVdl 6.39499e+02 > Dispersion correc. : dVdl 0.00000e+00 > > And I read : dVpot/dlambda = 3.62310e+02, instead of 3.70e+02. > > There is no PME in this sim. > > What did I forget ? > > Many thanks in advance, > > Michaël Bon > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: not available > Type: application/ms-tnef > Size: 2833 bytes > Desc: not available > Url : > http://www.gromacs.org/pipermail/gmx-users/attachments/20080129/a5603dbe/attachment-0001.bin > > ------------------------------ > > Message: 3 > Date: Tue, 29 Jan 2008 10:32:08 +0100 > From: Berk Hess <[EMAIL PROTECTED]> > Subject: [gmx-users] RE: RE : FEP : separating components of dgdl > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > > > > ---------------------------------------- > > Date: Tue, 29 Jan 2008 10:24:57 +0100 > > From: [EMAIL PROTECTED] > > To: [email protected] > > Subject: RE : FEP : separating components of dgdl > > > > > > Thanks for the quick reply. > > > > I have an other question : I ran a quick simulation on a single node using > > mdrun -sepdvdl and the components are written in > > the .log file. But the final value of dVpot/dlambda doesn't seem to be the > > sum of the components above. Example for some step: > > > > VdW and Coulomb SR : dVdl -2.72859e+02 > > Angle : dVdl 3.56537e+00 > > Proper Dih. : dVdl -7.31260e-03 > > Ryckaert-Bell. : dVdl -1.13654e-01 > > LJ-14 + Coulomb-14 : dVdl 6.39499e+02 > > Dispersion correc. : dVdl 0.00000e+00 > > > > And I read : dVpot/dlambda = 3.62310e+02, instead of 3.70e+02. > > > > There is no PME in this sim. > > > > What did I forget ? > > I assume you are running single processor. > The terms are per processor. > > I think that the only contributions that are no added are: > constraints, only when you change constraint lengths, > kinetic energy, only when you change masses. > > So do you change constraint lengths or masses? > > Berk. > > _________________________________________________________________ > Express yourself instantly with MSN Messenger! Download today it's FREE! > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ > > ------------------------------ > > Message: 4 > Date: Tue, 29 Jan 2008 10:47:45 +0100 > From: "Xavier Periole" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] dihedral restraints wiki section > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain;charset=utf-8;format="flowed" > > > > > Thank you for your help about performing dihedral restraints. Would you > >please kindly explain to me how I can measure the value of dihedral angles > >between two amin acids (I mean C'-N-C-C' and N-C-C'-N). > > Thank you in advance for your valuable aid. > > Well this should really be easy to find out! check out the manual, > there is section ANALYSIS ... g_angle is one option. > > > > > Behnoush > > > > ----- Original Message ----- > >From: "chris neale" <[EMAIL PROTECTED]> > > To: [email protected] > > Sent: Sunday, January 27, 2008 11:49:42 PM (GMT+0330) Asia/Tehran > > Subject: [gmx-users] dihedral restraints wiki section > > > > I have added a section on dihedral restraints to the wiki. > > > > http://wiki.gromacs.org/index.php/Dihedral_Restraints > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > ----------------------------------------------------- > XAvier Periole - PhD > > NMR & Molecular Dynamics Group > University of Groningen > The Netherlands > http://md.chem.rug.nl/~periole > ----------------------------------------------------- > > > ------------------------------ > > Message: 5 > Date: Tue, 29 Jan 2008 15:21:37 +0530 > From: "Nabajyoti Goswami" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] GROMACS ON CYGWIN. > To: "Discussion list for GROMACS users" <[email protected]> > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > If you are in windows and want to use gromacs by cygwin I suggest you to use > the window version of gromacs. place all gromacs executable into > C:/cygwin/home/bin *or* C:/windows/system32. It must work. > > On Jan 28, 2008 8:29 AM, Mark Abraham <[EMAIL PROTECTED]> wrote: > > > DAVID RINCON wrote: > > > Good morning people, > > > > > > I want to install gromacs on my laptop and I have installed cygwin and > > > some necessery gromacs libraries as fftw. But, when I am going to > > install, > > > > > > glibc > > > > > > just in the first step with ./configure. That broke down. :S > > > > Imagine I rang my car mechanic and told him that the car was borken and > > the spare tyre was making a weird noise, and asked him what was wrong... > > He'd ask me to bring him the car or describe the problem better. :-) > > > > > Someone has installed gromacs on their computers? > > > How can I do it? > > > > Start here http://wiki.gromacs.org/index.php/GROMACS_on_Windows and > > check out the general advice here > > http://www.catb.org/~esr/faqs/smart-questions.html<http://www.catb.org/%7Eesr/faqs/smart-questions.html> > > > > Mark > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > Regads, > Nabajyoti Goswami > > > > > > > > > > > > > Ph.D Student. > Center for Biotechnology, > Anna University, > Chennai-600025 > Tamil Nadu. > Mobile: 09840487093 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20080129/c0bd88c7/attachment-0001.html > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > [email protected] > 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 45, Issue 116 > ****************************************** > _________________________________________________________________ Express yourself instantly with MSN Messenger! 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