[gmx-users] overcome the integration problem (installing CVS)
Shalom all, To my best understanding, there is a correction to the single precision integration problem (A common, avoidable source of error in molecular dynamics integrators J. Chem. Phys. 126, 046101 (2007).) at the CVS. I want to know were can I get it and how to install it. First, the GROMACS site is down now. Second from the bit I have read, it is not clear to me how to install the stable CVS and not an experimentally version. Best, Itamar --- Prediction is very difficult, especially about the future - Niels Bohr === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | |Molecular Dynamics Group | School of Molecular and Microbial Sciences (SMMS) | Chemistry Building (#68) | The University of Queensland | St. Lucia Campus, Brisbane, QLD 4067 | Australia | | Tel: +61 7 3365 9922 | Fax: +61 7 3365 3872 | E-mail: [EMAIL PROTECTED] | Web page: http://www.uq.edu.au/~uqikass/ | Personal web page: http://thekassfamily.blogspot.com/ Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland ___ gmx-users mailing listgmx-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
Re: [gmx-users] overcome the integration problem (installing CVS)
On 4/11/2007 5:52 PM, Dr Itamar Kass wrote: Shalom all, To my best understanding, there is a correction to the single precision integration problem (A common, avoidable source of error in molecular dynamics integrators J. Chem. Phys. 126, 046101 (2007).) at the CVS. I want to know were can I get it and how to install it. First, the GROMACS site is down now. Second from the bit I have read, it is not clear to me how to install the stable CVS and not an experimentally version. Stable version: cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs login cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co -r release-3-3-patches gmx HEAD Branch cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs login cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co gmx Best, Itamar --- Prediction is very difficult, especially about the future - Niels Bohr === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | |Molecular Dynamics Group | School of Molecular and Microbial Sciences (SMMS) | Chemistry Building (#68) | The University of Queensland | St. Lucia Campus, Brisbane, QLD 4067 | Australia | | Tel: +61 7 3365 9922 | Fax: +61 7 3365 3872 | E-mail: [EMAIL PROTECTED] | Web page: http://www.uq.edu.au/~uqikass/ | Personal web page: http://thekassfamily.blogspot.com/ Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland ___ gmx-users mailing listgmx-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 listgmx-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
Re: [gmx-users] overcome the integration problem (installing CVS)
Yang Ye wrote: On 4/11/2007 5:52 PM, Dr Itamar Kass wrote: Shalom all, To my best understanding, there is a correction to the single precision integration problem (A common, avoidable source of error in molecular dynamics integrators J. Chem. Phys. 126, 046101 (2007).) at the CVS. I want to know were can I get it and how to install it. First, the GROMACS site is down now. Second from the bit I have read, it is not clear to me how to install the stable CVS and not an experimentally version. Stable version: cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs login cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co -r release-3-3-patches gmx HEAD Branch cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs login cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co gmx Best, Itamar The stable version does not have the fix (because it will change results). -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-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
Re: [gmx-users] overcome the integration problem (installing CVS)
From: David van der Spoel [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] overcome the integration problem (installing CVS) Date: Wed, 11 Apr 2007 12:13:13 +0200 Yang Ye wrote: On 4/11/2007 5:52 PM, Dr Itamar Kass wrote: Shalom all, To my best understanding, there is a correction to the single precision integration problem (A common, avoidable source of error in molecular dynamics integrators J. Chem. Phys. 126, 046101 (2007).) at the CVS. I want to know were can I get it and how to install it. First, the GROMACS site is down now. Second from the bit I have read, it is not clear to me how to install the stable CVS and not an experimentally version. Stable version: cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs login cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co -r release-3-3-patches gmx HEAD Branch cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs login cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co gmx Best, Itamar The stable version does not have the fix (because it will change results). -- David. I would like to add that for a constant temperature ensemble the effect of this fix is neglegible. It is only useful for constant NVE simulations. Berk. _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-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
Re: [gmx-users] overcome the integration problem (installing CVS)
Hi, all- I would like to add that for a constant temperature ensemble the effect of this fix is neglegible. It is only useful for constant NVE simulations. Berk. I think this might need some qualifications. If the constant temperature dynamics are based inherently on NVE dynamics, they must be affected similarly. For example, for Nose-Hoover thermostats, there exists a conserved quantity. I would expect that this fix would also improve that conserved quantity, wouldn't it? One feature that would be useful is that for any algorithm that has a conserved energy-like quantity, there should be an entry in the .edr file with that quantity. It would be a useful check for algorithmic consistency. I don't think this is yet in GROMACS, though I could be wrong -- I haven't examined the CVS that recently. Best, Michael Shirts Research Fellow Department of Chemistry Columbia University ___ gmx-users mailing listgmx-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
Re: [gmx-users] overcome the integration problem (installing CVS)
Michael Shirts wrote: Hi, all- I would like to add that for a constant temperature ensemble the effect of this fix is neglegible. It is only useful for constant NVE simulations. Berk. I think this might need some qualifications. If the constant temperature dynamics are based inherently on NVE dynamics, they must be affected similarly. For example, for Nose-Hoover thermostats, there exists a conserved quantity. I would expect that this fix would also improve that conserved quantity, wouldn't it? One feature that would be useful is that for any algorithm that has a conserved energy-like quantity, there should be an entry in the .edr file with that quantity. It would be a useful check for algorithmic consistency. I don't think this is yet in GROMACS, though I could be wrong -- I haven't examined the CVS that recently. How about total energy? In tends to be constant in NVE simulations. I don't know what the conserved property would be in an NVT simulation. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-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
