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: gmx-users@gromacs.org Objet : gmx-users Digest, Vol 45, Issue 116 Send gmx-users mailing list submissions to gmx-users@gromacs.org 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 <gmx-users@gromacs.org> 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: gmx-users@gromacs.org 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 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 [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: <gmx-users@gromacs.org> 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 <gmx-users@gromacs.org> 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: gmx-users@gromacs.org > 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 <gmx-users@gromacs.org> 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: gmx-users@gromacs.org > 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 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 [EMAIL PROTECTED] > 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 [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" <gmx-users@gromacs.org> 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 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 [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 gmx-users@gromacs.org 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 ******************************************
<<winmail.dat>>
_______________________________________________ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php