[gmx-users] COM of a molecule
Hi I want to determine center of mass position of a molecule given an index of any of the atoms of the molecule. One may be able to do this if given an atom index one can access indices and hence the position of all other atoms belonging to the same molecule. Is there a way to do this in a program using gmx library? Thanks Sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] AdRess generic kernel for non-bonded interactions
Hi I have a question regarding how non-bonded interactions are determined when running AdRess simulations in Gromacs. In the case in which I have defined all of the system as explicit, i.e., all-atom and NO CG region, are the forces computed in the same manner as if it were doing a normal/all-atom gromacs simulations with generic non-bonded kernel, i.e., GMX_NB_GENERIC=1. Thanks Sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] velocity-verlet giving nans
Hi I first performed a simulation using leap-frog integrator, which went well and got the expected results. For post-processing I want velocities at full time step, but, as per my understanding, leap-frog computes and writes velocities at half-time step. Therefore, I just changed integrator from 'md' to 'md-vv', i.e., velocity verlet. Unfortunately, after this change in .mdp file (i.e. keeping all other settings exactly same as previous leap-frog run) when I run 'mdrun' I am getting 'nan' in output from the first step itself. So I am wondering what could be the reason for this behavior of 'md-vv' integrator. Thanks Sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] double sum over neighbor list
Hi I am tyring to compute total virial, i.e. sum_i sum_j (rij*Fij). To achieve this, I am making modifications in the gmx_nb_generic_kernel() function in nb_generic.c. In it, I see that atoms I and j are accessed from neighbor lists to determine forces on atom I . My question is that in this loop do I have to take care of double counting pair forces, i.e. will the pair of atom I and j be accessed twice or just once? Thanks Sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] point in source code to access atom position
Hi I want to store Z coordinates of atoms at the beginning of each time step when I am doing 'mdrun -rerun'. I am not able to find the line and file in the source code where I can implement this. Can anyone please help me with that? Thanks Sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] stable branch using git
Thanks Justin and Mark I think I would checkout and create a branch from v4.6 tag. One more thing, would it be an issue if I install mulitple version's/branche's binaries and libraries in the same folder with branch specific suffixes to distinguish between them? Thanks Sikandar On Wed, May 1, 2013 at 3:25 AM, Mark Abraham mark.j.abra...@gmail.comwrote: On Wed, May 1, 2013 at 2:50 AM, Sikandar Mashayak symasha...@gmail.com wrote: Hi Justin Thanks for explanation. But I am a bit confused because I am new to git. When I check out release-4-6 branch, the source code should be the same as the one in tarball from Gromacs website, right? No. The tarball is made from a particular commit and that commit has a git tag identifying it (though I did mess that up slightly for 4.6.1). History then continues in the branch. Its head commit only coincides with a tag immediately after a release. When I run git status I get # On branch release-4-6 nothing to commit (working directory clean), I believe that means I have the released version of the code. No, you have the head of the development branch from which releases are currently being made. Do check out some git tutorial material. The reason I am doing this is that I want to have just one directory for gromacs with subdirectories for its src, build and binaries. And in future, instead of downloading new releases, I want to just pull the changes and re-build. In principle, that workflow can work, but you need to (e.g.) use git checkout v4.6 to check out the commit we tagged when we built the 4.6 tarball. Also, I plan to clone the same src directory on my different machines, so that I can have the same version on all machines. You can do similar things with the tarball, so I don't see what you're gaining :-) Mark Hopefully, in the future I may start doing some modifications here n there. Thanks Sikandar On Tue, Apr 30, 2013 at 7:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/30/13 8:28 PM, Sikandar Mashayak wrote: Thanks Justin. I replaced release-4-5-patches with release-4-6 while checking out the branch. When I installed it and checked the version string I get VERSION 4.6.2-dev-20130429-d13fc48. Does that mean I got the version which is still under development and not stable and tested? Should I be concerned using it to do a production run? We generally discourage anyone from doing production work with anything that's not an official release. Anything you pull from the git repo is a work in progress. Periodic releases are generated when the code is believed to be production-ready. We do code review and build testing and each patch is as reliable as we believe it to be :) The reference to a stable branch is probably a bit misleading, but the master branch is currently undergoing large-scale changes, leaving it perhaps a bit more unstable than release-4-6. The release-4-6 branch is the one from which the development team is producing actual releases. If you want the latest version, just download the 4.6.1 tarball from the Gromacs website. Version 4.6.2 should be out fairly soon, but there are some issues that are still being cleaned up. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send
Re: [gmx-users] local pressure
Thanks Xavier Can you please elaborate on how to use and post-process the local pressure version of gromacs? Do you have any examples or reference article? May be you can create a HowTo wiki as Justin suggested, it would be of great help. Thanks Sikandar On Wed, May 1, 2013 at 5:03 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/1/13 5:12 AM, XAvier Periole wrote: The use of the original code is quite straightforward, the post processing is a bit more confusing but quite accessible. That would be a great topic for a wiki How-To. We have been using this code (the one available on the site) and related version in the lab and we definitely would find it very sad to not keep this feature available in GROMACS. I never said it would go away, but given the fact that there have been no updates to the git branch in over 3 years, it's simply unlikely that anyone has cared to move it forward. If someone wants to update the code to be compatible with 4.6, that would be a welcome contribution. Lack of any request for improvements and inclusion in an official release has likely led to the decline in interest from the development team. If you want something included, you should file a feature request on redmine.gromacs.org - it's the only official way we keep track of fixes and features. If it's not there, it likely won't get addressed until one of the developers has a compelling need to work on it. -Justin On May 1, 2013, at 2:34 AM, Justin Lemkul jalem...@vt.edu wrote: On 4/30/13 8:01 PM, Sikandar Mashayak wrote: Hi I found the branch of gromacs code called localpressure-4.0 at http://redmine.gromacs.org/**projects/gromacs/repository/** show?rev=localpressure-4-0http://redmine.gromacs.org/projects/gromacs/repository/show?rev=localpressure-4-0 . I am wondering whether this code can compute the spatial variation of pressure in given system. And if it does, how stable is this branch? Are there any known issues with it? And any particular reason this is not included in main gromacs releases? Lack of documentation has made it very difficult to use, it is extremely slow, and no one ever asks about it except once every few years. All of those factors make it unlikely to ever incorporate into an actual release. Given that the development process has gone on for years in the absence of any real interest in the localpressure branch, it's probably more trouble than it's worth to get it up and running effectively. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] local pressure
Thanks Xavier, I will give it a try. On Wed, May 1, 2013 at 10:56 AM, XAvier Periole x.peri...@rug.nl wrote: Well I am not the expert. O.H.S. Ollila, M. Louhivuori and E. Lindahl are :)). The paper related to the use would be: Ollila et al, PRL 102, 078101 (2009) Ollila et al, Biophysical Journal (100)1651–59 On May 1, 2013, at 5:48 PM, Sikandar Mashayak symasha...@gmail.com wrote: Thanks Xavier Can you please elaborate on how to use and post-process the local pressure version of gromacs? Do you have any examples or reference article? May be you can create a HowTo wiki as Justin suggested, it would be of great help. Thanks Sikandar On Wed, May 1, 2013 at 5:03 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/1/13 5:12 AM, XAvier Periole wrote: The use of the original code is quite straightforward, the post processing is a bit more confusing but quite accessible. That would be a great topic for a wiki How-To. We have been using this code (the one available on the site) and related version in the lab and we definitely would find it very sad to not keep this feature available in GROMACS. I never said it would go away, but given the fact that there have been no updates to the git branch in over 3 years, it's simply unlikely that anyone has cared to move it forward. If someone wants to update the code to be compatible with 4.6, that would be a welcome contribution. Lack of any request for improvements and inclusion in an official release has likely led to the decline in interest from the development team. If you want something included, you should file a feature request on redmine.gromacs.org - it's the only official way we keep track of fixes and features. If it's not there, it likely won't get addressed until one of the developers has a compelling need to work on it. -Justin On May 1, 2013, at 2:34 AM, Justin Lemkul jalem...@vt.edu wrote: On 4/30/13 8:01 PM, Sikandar Mashayak wrote: Hi I found the branch of gromacs code called localpressure-4.0 at http://redmine.gromacs.org/**projects/gromacs/repository/** show?rev=localpressure-4-0 http://redmine.gromacs.org/projects/gromacs/repository/show?rev=localpressure-4-0 . I am wondering whether this code can compute the spatial variation of pressure in given system. And if it does, how stable is this branch? Are there any known issues with it? And any particular reason this is not included in main gromacs releases? Lack of documentation has made it very difficult to use, it is extremely slow, and no one ever asks about it except once every few years. All of those factors make it unlikely to ever incorporate into an actual release. Given that the development process has gone on for years in the absence of any real interest in the localpressure branch, it's probably more trouble than it's worth to get it up and running effectively. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search
Re: [gmx-users] local pressure
Ok, I did rerun with local pressure mdrun, and got pressure.dat* files in binary format. how do I proceed from here? Any utility to analyze or post-process this? On Wed, May 1, 2013 at 11:11 AM, Sikandar Mashayak symasha...@gmail.comwrote: Thanks Xavier, I will give it a try. On Wed, May 1, 2013 at 10:56 AM, XAvier Periole x.peri...@rug.nl wrote: Well I am not the expert. O.H.S. Ollila, M. Louhivuori and E. Lindahl are :)). The paper related to the use would be: Ollila et al, PRL 102, 078101 (2009) Ollila et al, Biophysical Journal (100)1651–59 On May 1, 2013, at 5:48 PM, Sikandar Mashayak symasha...@gmail.com wrote: Thanks Xavier Can you please elaborate on how to use and post-process the local pressure version of gromacs? Do you have any examples or reference article? May be you can create a HowTo wiki as Justin suggested, it would be of great help. Thanks Sikandar On Wed, May 1, 2013 at 5:03 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/1/13 5:12 AM, XAvier Periole wrote: The use of the original code is quite straightforward, the post processing is a bit more confusing but quite accessible. That would be a great topic for a wiki How-To. We have been using this code (the one available on the site) and related version in the lab and we definitely would find it very sad to not keep this feature available in GROMACS. I never said it would go away, but given the fact that there have been no updates to the git branch in over 3 years, it's simply unlikely that anyone has cared to move it forward. If someone wants to update the code to be compatible with 4.6, that would be a welcome contribution. Lack of any request for improvements and inclusion in an official release has likely led to the decline in interest from the development team. If you want something included, you should file a feature request on redmine.gromacs.org - it's the only official way we keep track of fixes and features. If it's not there, it likely won't get addressed until one of the developers has a compelling need to work on it. -Justin On May 1, 2013, at 2:34 AM, Justin Lemkul jalem...@vt.edu wrote: On 4/30/13 8:01 PM, Sikandar Mashayak wrote: Hi I found the branch of gromacs code called localpressure-4.0 at http://redmine.gromacs.org/**projects/gromacs/repository/** show?rev=localpressure-4-0 http://redmine.gromacs.org/projects/gromacs/repository/show?rev=localpressure-4-0 . I am wondering whether this code can compute the spatial variation of pressure in given system. And if it does, how stable is this branch? Are there any known issues with it? And any particular reason this is not included in main gromacs releases? Lack of documentation has made it very difficult to use, it is extremely slow, and no one ever asks about it except once every few years. All of those factors make it unlikely to ever incorporate into an actual release. Given that the development process has gone on for years in the absence of any real interest in the localpressure branch, it's probably more trouble than it's worth to get it up and running effectively. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ
[gmx-users] stable branch using git
Hi I am following the git tutorial for the novice. It says to check out stable version one should use git checkout --track -b release-4-5-patches origin/release-4-5-patches Is there stable branch for 4.6? If yes, how do get it? I tried replacing 4-5 by 4-6 but I get the error: fatal: git checkout: updating paths is incompatible with switching branches. Did you intend to checkout 'origin/release-4-6-patches' which can not be resolved as commit? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] local pressure
Hi I found the branch of gromacs code called localpressure-4.0 at http://redmine.gromacs.org/projects/gromacs/repository/show?rev=localpressure-4-0. I am wondering whether this code can compute the spatial variation of pressure in given system. And if it does, how stable is this branch? Are there any known issues with it? And any particular reason this is not included in main gromacs releases? Thanks Sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] stable branch using git
Thanks Justin. I replaced release-4-5-patches with release-4-6 while checking out the branch. When I installed it and checked the version string I get VERSION 4.6.2-dev-20130429-d13fc48. Does that mean I got the version which is still under development and not stable and tested? Should I be concerned using it to do a production run? Thanks Sikandar On Tue, Apr 30, 2013 at 2:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/30/13 3:03 PM, Sikandar Mashayak wrote: Hi I am following the git tutorial for the novice. It says to check out stable version one should use git checkout --track -b release-4-5-patches origin/release-4-5-patches Is there stable branch for 4.6? If yes, how do get it? I tried replacing 4-5 by 4-6 but I get the error: fatal: git checkout: updating paths is incompatible with switching branches. Did you intend to checkout 'origin/release-4-6-patches' which can not be resolved as commit? There is no release-4-6-patches branch. It's just release-4-6. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] stable branch using git
Hi Justin Thanks for explanation. But I am a bit confused because I am new to git. When I check out release-4-6 branch, the source code should be the same as the one in tarball from Gromacs website, right? When I run git status I get # On branch release-4-6 nothing to commit (working directory clean), I believe that means I have the released version of the code. The reason I am doing this is that I want to have just one directory for gromacs with subdirectories for its src, build and binaries. And in future, instead of downloading new releases, I want to just pull the changes and re-build. Also, I plan to clone the same src directory on my different machines, so that I can have the same version on all machines. Hopefully, in the future I may start doing some modifications here n there. Thanks Sikandar On Tue, Apr 30, 2013 at 7:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/30/13 8:28 PM, Sikandar Mashayak wrote: Thanks Justin. I replaced release-4-5-patches with release-4-6 while checking out the branch. When I installed it and checked the version string I get VERSION 4.6.2-dev-20130429-d13fc48. Does that mean I got the version which is still under development and not stable and tested? Should I be concerned using it to do a production run? We generally discourage anyone from doing production work with anything that's not an official release. Anything you pull from the git repo is a work in progress. Periodic releases are generated when the code is believed to be production-ready. We do code review and build testing and each patch is as reliable as we believe it to be :) The reference to a stable branch is probably a bit misleading, but the master branch is currently undergoing large-scale changes, leaving it perhaps a bit more unstable than release-4-6. The release-4-6 branch is the one from which the development team is producing actual releases. If you want the latest version, just download the 4.6.1 tarball from the Gromacs website. Version 4.6.2 should be out fairly soon, but there are some issues that are still being cleaned up. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Memory requirement to store trajectories
Hi I would like to determine an estimate of hard disk space required to perform a typical MD simulation using gromacs. To do so, I am thinking of first finding how many bytes are required to store single atom's position, velocity and force in .trr file for a single frame, and then determine total bytes required by multiplying it by total number of atoms and required number of time-frames for a given system. So, can anyone give me an estimate of number of bytes required to store single atom's position, velocity and force in .trr file of gromacs? Also please suggest me if there is any other better approach to determine an estimate of hard disk space required. Thanks Sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] about tabulated potentials
From your system information, I understand that you need to specify tabulated potentials between atoms P and P, and between atoms C and P, and so on. To achieve this, you need to create energy groups with atom types P and C, and specify energygrp_table options in the grompp such as following energygrps = P C ; (and rest of the groups in your system, you will need to specify index file containing energy groups ) energygrp_table = P P P C so now mdrun looks for table_P_P.xvg and table_P_C.xvg in the run directory, and uses it for P-P and P-C interactions, whereas for all other interactions default table.xvg file is used. I hope this helps. Regards Sikandar On Tue, Nov 15, 2011 at 2:49 PM, Liu, Liang liu4...@gmail.com wrote: I am trying to use a serial of tabulated potentials, which are the functions of the distance between atoms and the names are table.xvg, table_P_P.xvg, table_C_P.xvg, etc., to do the energy minimization of some RNA structures. The procedure I apply is as following: pdb2gmx -f rna.pdb -o conf.pdb -ff amber03 -water spce editconf -bt octahedron -f conf.pdb -o box.pdb -d 1.0 genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top grompp -f em.mdp -c water.pdb -p topol.top -o em.tpr -maxwarn 2 mdrun -v -s em.tpr -c em.pdb -table table.xvg And the em.mdp file is: cpp = /usr/bin/cpp; Preprocessor include = -I../top; Directories to include in the topology format define = -DFLEX_SPC integrator = steep ; Algorithm options dt = 0.002; ps ! ; run control, the time step nsteps = 1000; run steps, simulation length = dt*nsteps nstenergy = 10 ; Write energies to disk every nstenergy steps nstxtcout = 10 ; Write coordinates to disk every nstxtcout steps xtc_grps= RNA ; Which coordinate group(s) to write to disk energygrps = RNA ; Whici energy group(s) to write to disk nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid; Method to determine neighbor list and long range forces (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) vdw-type= user coulombtype = user; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Walls cut-off constraints = none pbc = xyz emtol = 5000.0 emstep = 0.01 All the procedure and file are right? Thanks. -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] gromacs command help text
Hi All gromacs commands print the help text every time they are run. Is there a way to tell gromacs command not to print help text? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs command help text
Hey Justin, -quiet works thanks --- sikandar On Thu, Oct 20, 2011 at 10:22 AM, Justin A. Lemkul jalem...@vt.edu wrote: Sikandar Mashayak wrote: Hi All gromacs commands print the help text every time they are run. Is there a way to tell gromacs command not to print help text? Use the -quiet option. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Pressure estimation from NVT
Hi @ Dallas and Justin Do you mean that for gromacs version 4.5.3 averages computed using g_energy may be flawed? And are you suggesting to compute average pressure explicitly from instantaneous P values in trajectory? @ Mark Thanks for suggestion. I am doing 500 ps of equilibration and 10 ns of production runs with 2141 molecules. So the important point that I want to understand is that if I use the right averaging or newer gromacs version, and do large system with longer production runs, how accurate is the estimate of pressure values from bulk water NVT simulations? thanks sikandar On Mon, Sep 26, 2011 at 8:51 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 27/09/2011 3:48 AM, Sikandar Mashayak wrote: Hi I am trying to determine pressure of water at given density and temperature using SPC/E water model. To achieve this, I am doing NVT bulk simulations and then using g_energy I get average pressure values. The question I have is how accurate these average pressure predictions are? e.g. I get average pressure of 185 bar for 300 K and 1 g/cm^3 water density, but theoretical value for it is around 1 bar. What are the possible reasons for this much deviation from theoretical value? Is there anything wrong with my set up? I am using 2141 water molecules in 4*4*4 periodic box, Nose-Hoover thermostat with 0.2ps time constant , MD algorithm with 1fs time-step, LJ with 1.5 nm cut off and PME for electrostatics. The length of your simulation, and the absence of the equilibration period from your data collection are also critical factors in obtaining accurate converged averages, but usually neglected when people report what might be anomalies... please see http://www.gromacs.org/** Documentation/Terminology/**Pressurehttp://www.gromacs.org/Documentation/Terminology/Pressure Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Pressure estimation from NVT
Hi I am trying to determine pressure of water at given density and temperature using SPC/E water model. To achieve this, I am doing NVT bulk simulations and then using g_energy I get average pressure values. The question I have is how accurate these average pressure predictions are? e.g. I get average pressure of 185 bar for 300 K and 1 g/cm^3 water density, but theoretical value for it is around 1 bar. What are the possible reasons for this much deviation from theoretical value? Is there anything wrong with my set up? I am using 2141 water molecules in 4*4*4 periodic box, Nose-Hoover thermostat with 0.2ps time constant , MD algorithm with 1fs time-step, LJ with 1.5 nm cut off and PME for electrostatics. thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] decomposing the energy
Hey Mark Do you mean removing all bond definitions from topology file, when you say well constructed topology to exclude all bonded-interactions in rerun? thanks sikandar On Sat, May 14, 2011 at 8:01 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 14/05/2011 10:52 PM, XAvier Periole wrote: Two things you have to be careful about: 1- use trr trajectory files. xtc precision is not sufficient and it will give a lot of discrepancies at least for the bonded terms. 2- set the nstlist to 1 as the neiboring list should be undated for each frame and not every 5/10 as it is normally set in a regular mdp file. Reruns do neighbour searching every frame, regardless. Mark On May 14, 2011, at 1:11 PM, Justin A. Lemkul wrote: Ramachandran G wrote: Hello gmx users: I did 1ns simulation for my system and have the trajectory and energy files. Now i want to see the energy of some specific residues. So, i decompose(separated) the energy groups and edited the mdp file. Using the mdp file, i created a new tpr file and rerun the mdrun using the trajectory file. But when i compared the total energy between the old and new one, it differs a lot. I am doing some mistakes somewhere. Can anyone help me please. Thanks. Maybe, maybe not. Without seeing the .mdp settings and the data that you're looking at, all anyone can do is guess. You also haven't stated what type of trajectory (i.e. .xtc or .trr) you're using as -rerun input. If you're using an .xtc file, there is no velocity information, so any property related to velocities (most notably kinetic energy, but several others as well) will be zero. I suspect this is probably where the discrepancy is, but it is not a problem. Using energygrps is only useful for decomposing short-range nonbonded energy terms, nothing else. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RMSD with Vsite vs No Vsites
well the deviations are about more than 0.5 nm.. On Fri, May 6, 2011 at 1:49 AM, Peter C. Lai p...@uab.edu wrote: On 2011-05-05 11:21:54AM -0500, Sikandar Mashayak wrote: Hi As a test case, I did two simulations one the usual Protein in Water and other with Vsites at COM of each monomer but these Vsites dont interact with anyone else. I was expecting results of these two should match almost exactly, but when I compare the rmsd for Protein there seems to be discrepancy. I once again checked my Vsites definitions and set up, there doesnt seem to be any error in definition as per my understanding. Is there any other reason that may be causing the mismatch? Or I may have done something wrong in the setting up Vsites simulations. thanks sikandar how large are the RMSD deviations? are they statistically significant for your needs? (i.e. if you only are about 1A scales, then RMSD differences 0.05nm would be meaningless... -- === Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | === -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] virtual sites set up for topology file
Yes, since sigma and epsilon are zero for VS then interactions between and VS-VS and VS-(any other atom) would result in zero force. Since you explicitly define the interaction between VS-C3, combination rule won't be used and C6(VS_C3) and C12(VS_C3) will be computed as per sigma(VS_C3) epsilon(VS_C3) you defined under [nonbond_params] cheers sikandar On Fri, May 6, 2011 at 9:03 AM, Gavin Melaugh gmelaug...@qub.ac.uk wrote: Am I correct in saying now, from the following topology (exerpts), that the virtual site VS will only interact with C3? I guess I don't have to give the atom indices of this interaction in the pair list which I use only for 1_4 interactions? Can I use sigma and epsilon in the nonbond_params directive like in atomtypes. ;Parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.390500 0.732200 C2 14.027000 0.00 A 0.390500 0.493712 VS 0.0 0.0V 0.0 0.0 [nonbond_params] ;ij func sigmaepsilon VS C31 0.1 0.03153 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] virtual sites set up for topology file
yes it will... On Fri, May 6, 2011 at 11:02 AM, Gavin Melaugh gmelaug...@qub.ac.uk wrote: Cheers Sikandar I take it that because combination rule 3 (provide sigma and epsilon) is stated gromacs assumes that all values in nonbonding parameters are sigma and epsilon. I know this tp be tru for the atomtypes but does it filter down to all intermolecular interactions. Cheers Gavin Sikandar Mashayak wrote: Yes, since sigma and epsilon are zero for VS then interactions between and VS-VS and VS-(any other atom) would result in zero force. Since you explicitly define the interaction between VS-C3, combination rule won't be used and C6(VS_C3) and C12(VS_C3) will be computed as per sigma(VS_C3) epsilon(VS_C3) you defined under [nonbond_params] cheers sikandar On Fri, May 6, 2011 at 9:03 AM, Gavin Melaugh gmelaug...@qub.ac.uk mailto:gmelaug...@qub.ac.uk wrote: Am I correct in saying now, from the following topology (exerpts), that the virtual site VS will only interact with C3? I guess I don't have to give the atom indices of this interaction in the pair list which I use only for 1_4 interactions? Can I use sigma and epsilon in the nonbond_params directive like in atomtypes. ;Parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.390500 0.732200 C2 14.027000 0.00 A 0.390500 0.493712 VS 0.0 0.0V 0.0 0.0 [nonbond_params] ;ij func sigmaepsilon VS C31 0.1 0.03153 -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] virtual sites
yes, you can make virtual sites interact with only specific sites by using Energy Exclusion between energy groups. This can be done by defining energy groups for virtual sites and other atoms, then exclude or include the non-bonded interactions between them accordingly... On Thu, May 5, 2011 at 7:30 AM, Gavin Melaugh gmelaug...@qub.ac.uk wrote: Hi All Is it possible to have a virtual site interact with only specific atoms and not interact at all with everything else? Cheers Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] virtual sites
you can do it as following 1. create index file make_indx -f conf.gro -n index.ndx ( select VS and any other atoms you want lets say OTHERS) 2. in .mdp define energygrps VS OTHERS 3. exclude interactions by specifying energygrp_excl VS OTHERS in .mdp file for more you can refer to manual.. I hope it helps -- sikandar On Thu, May 5, 2011 at 11:00 AM, Gavin Melaugh gmelaug...@qub.ac.uk wrote: Hi Sikandar Cheers. How do you actually define the energy groups? Gavin Sikandar Mashayak wrote: yes, you can make virtual sites interact with only specific sites by using Energy Exclusion between energy groups. This can be done by defining energy groups for virtual sites and other atoms, then exclude or include the non-bonded interactions between them accordingly... On Thu, May 5, 2011 at 7:30 AM, Gavin Melaugh gmelaug...@qub.ac.uk mailto:gmelaug...@qub.ac.uk wrote: Hi All Is it possible to have a virtual site interact with only specific atoms and not interact at all with everything else? Cheers Gavin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RMSD with Vsite vs No Vsites
Hi As a test case, I did two simulations one the usual Protein in Water and other with Vsites at COM of each monomer but these Vsites dont interact with anyone else. I was expecting results of these two should match almost exactly, but when I compare the rmsd for Protein there seems to be discrepancy. I once again checked my Vsites definitions and set up, there doesnt seem to be any error in definition as per my understanding. Is there any other reason that may be causing the mismatch? Or I may have done something wrong in the setting up Vsites simulations. thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] virtual sites
hey another approach to do this without using energy group exclusion is to define non-bonded interactions parameter explicitly between atoms in ffnonbonded.itp file. You can specify sigma and epsilon to be zero in virtual sites atoms definition and specify individual pair interactions parameters using non-bonded interactions like following ... ; virtual site VS1 00 0 D 0 0 VS2 00 0 D 0 0 VS3 00 0 D 0 0 [ nonbond_params ] VS1 C 1 1.0 0.25 VS2 C 1 1.0 0.25 VS2 C 1 1.0 0.25 -- sikandar On Thu, May 5, 2011 at 11:47 AM, Gavin Melaugh gmelaug...@qub.ac.uk wrote: Hi Justin I do not intend to have charges on the sites. All I want is; when a CH3 group gets close to the site it feels a repulsive force. I have calculated a sigma and epsilon value for this interaction. Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin I am reading the manual at the moment. I want to include some virtual sites in my molecule so that only surrounding CH3s atom type C3 interact with then. All other atoms I don't want to interact with them. Do I create energy groups in the index file called say virtual sites and exclusions, and list all the indices of the atom types that I don't want to interact with the virtual site in one group and all the virtual sites in another. e.g [virtual sites] 17 18 19 20 [virtsite_exclus] 1 2 3 4 5 6 7 8 9 . In a general sense, yes, that's the right approach. Note that if any of these sites is charged and/or you're using PME, then this whole exclusion thing goes out the window, as has been discussed several times in recent days. Using energygrp_excl applies only to short-range nonbonded interactions. If you need complete exclusion, you may have to look into tabulated potentials if this is the case. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] virtual sites
in doing so .. by default all pair interactions with virtual sites would result in zero forces except those between atoms defined in [nonbond_params] On Thu, May 5, 2011 at 11:57 AM, Sikandar Mashayak symasha...@gmail.comwrote: hey another approach to do this without using energy group exclusion is to define non-bonded interactions parameter explicitly between atoms in ffnonbonded.itp file. You can specify sigma and epsilon to be zero in virtual sites atoms definition and specify individual pair interactions parameters using non-bonded interactions like following ... ; virtual site VS1 00 0 D 0 0 VS2 00 0 D 0 0 VS3 00 0 D 0 0 [ nonbond_params ] VS1 C 1 1.0 0.25 VS2 C 1 1.0 0.25 VS2 C 1 1.0 0.25 -- sikandar On Thu, May 5, 2011 at 11:47 AM, Gavin Melaugh gmelaug...@qub.ac.ukwrote: Hi Justin I do not intend to have charges on the sites. All I want is; when a CH3 group gets close to the site it feels a repulsive force. I have calculated a sigma and epsilon value for this interaction. Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin I am reading the manual at the moment. I want to include some virtual sites in my molecule so that only surrounding CH3s atom type C3 interact with then. All other atoms I don't want to interact with them. Do I create energy groups in the index file called say virtual sites and exclusions, and list all the indices of the atom types that I don't want to interact with the virtual site in one group and all the virtual sites in another. e.g [virtual sites] 17 18 19 20 [virtsite_exclus] 1 2 3 4 5 6 7 8 9 . In a general sense, yes, that's the right approach. Note that if any of these sites is charged and/or you're using PME, then this whole exclusion thing goes out the window, as has been discussed several times in recent days. Using energygrp_excl applies only to short-range nonbonded interactions. If you need complete exclusion, you may have to look into tabulated potentials if this is the case. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] excluding electrostatic interactions
Hi I want to compute only the non-bonded ( LJ + EL) interactions between Protein and Solvent and exclude non-bonded interactions between Protein Protein SOL SOL. But energy exclusion group does not necessarily exclude the non-bonded electrostatic interactions while using PME option for coulombtype. So I am just wondering if I were to compute electrostatic interactions between just Protein SOL with PME, how can I do that? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] excluding electrostatic interactions
yeah, it says PME cant be excluded using energy exclusion, so I am wondering about any other way to exclude it? On Tue, May 3, 2011 at 5:01 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sikandar Mashayak wrote: Hi I want to compute only the non-bonded ( LJ + EL) interactions between Protein and Solvent and exclude non-bonded interactions between Protein Protein SOL SOL. But energy exclusion group does not necessarily exclude the non-bonded electrostatic interactions while using PME option for coulombtype. So I am just wondering if I were to compute electrostatic interactions between just Protein SOL with PME, how can I do that? Hasn't this already been answered? http://lists.gromacs.org/pipermail/gmx-users/2011-April/060594.html -Justin thanks sikandar -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Virtual site at COM of more than 4 atoms
Hey Mark Using [virtual_sitesn] 39 2 34 35 36 37 38 seems to be working to define virtual sites at COM of group of atoms. thanks for the answer... sikandar On Mon, Apr 25, 2011 at 12:15 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/25/2011 2:49 PM, Sikandar Mashayak wrote: Hi I am not sure , even after reading the manual, about how to specify virtual site in topology file which is located at com of 5 atoms. If I were to specify it by using [ virutal_sitesn] then how to specify weights, so that vsite is at COM? Table 5.6 says you choose a COM vsite with function type 2. So I expect that [virtual_sitesn] 39 2 34 35 36 37 38 will make atom 39 a vsite formed from the COM of atoms 34-38. The manual is a bit deficient in this regard. Let us know how it goes, and I'll update the manual. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] tabulated potentials
Hi I want to try out different potentials using tabulated potential method. I am planning to specify sigma and epsilon such that C6 and C12 values will be 1.0 and in table.xvg file 6th and 7th columns will contain actual potential and force values, whereas columns 2-5 will be zero. As per manual, all columns in table.xvg should contain meaningful nonzero values, though they are not being used. Does that mean having zeros in columns would give erroneous results? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] tabulated potentials for non-bonded interactions
Hi Is it possible to use use specified potentials only for vdw type non-bonded interactions while keeping usual PME,bonded, pairs interactions? When I specifiy User for vdwtype force in .mdp file, I am observing that mdrun expects table for bonded interactions also through -tableb option and by default uses table.xvg. Is there any way to avoid this? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Load imbalance vs accuracy
Hi Is load imbalance during mdrun only a performance issue or it affects accuracy of run as well? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Virtual site at COM of more than 4 atoms
Hi I am not sure , even after reading the manual, about how to specify virtual site in topology file which is located at com of 5 atoms. If I were to specify it by using [ virutal_sitesn] then how to specify weights, so that vsite is at COM? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: energy group exclusions
Yes, 7.3.19 says that all non-nonbonded interactions are excluded within energy_exclusion groups. What I really trying is to get forces on water atoms only because of water water interactions and I want force on protein atoms to be zero, so I do md rerun with energy_exclusion as PROTEIN PROTEIN PROTEIN SOL and also remove any bond interaction information from .top file for protein, but still I get force values on protein atoms. Not sure whats going wrong? thanks sikandar On Tue, Apr 19, 2011 at 12:04 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/19/2011 2:57 PM, Sikandar Mashayak wrote: so that means if I define a index group GRP and energy exclusion GRP GRP then all the non-boned interactions between atoms belonging to GRP group are excluded? What does manual 7.3.19 say? Mark On Mon, Apr 18, 2011 at 7:43 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/18/2011 1:43 PM, Sikandar Mashayak wrote: Also, what about non-bonded interactions within the protein? Does exclusion group only exclude the non-bonded interactions between two different molecules and non-bonded interactions within the single molecule atoms are still computed? The sets of atoms for energy groups and such exclusions are defined by the index groups, not molecules. See manual 7.3 and wherever it talks about groups in an early chapter. On Sun, Apr 17, 2011 at 10:38 PM, Sikandar Mashayak symasha...@gmail.com wrote: Hi When we define energy group exclusions e.g. like in manual energygrp excl = Protein Protein SOL SOL and do md rerun, then only non-bonded interactions between Protein and SOL are computed. I am wondering what happens to bonded interactions within the protein, do they contribute to energies even though we have excluded protein-protein interactions? Bonded interactions are unaffected, as you will see if you try it. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: energy group exclusions
Also, in the case of spc/e bulk water when I do md rerun with SOL SOL exlcusion I see forces on water atoms, however I was expecting it to be zero. On Tue, Apr 19, 2011 at 11:12 AM, Sikandar Mashayak symasha...@gmail.comwrote: Yes, 7.3.19 says that all non-nonbonded interactions are excluded within energy_exclusion groups. What I really trying is to get forces on water atoms only because of water water interactions and I want force on protein atoms to be zero, so I do md rerun with energy_exclusion as PROTEIN PROTEIN PROTEIN SOL and also remove any bond interaction information from .top file for protein, but still I get force values on protein atoms. Not sure whats going wrong? thanks sikandar On Tue, Apr 19, 2011 at 12:04 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/19/2011 2:57 PM, Sikandar Mashayak wrote: so that means if I define a index group GRP and energy exclusion GRP GRP then all the non-boned interactions between atoms belonging to GRP group are excluded? What does manual 7.3.19 say? Mark On Mon, Apr 18, 2011 at 7:43 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/18/2011 1:43 PM, Sikandar Mashayak wrote: Also, what about non-bonded interactions within the protein? Does exclusion group only exclude the non-bonded interactions between two different molecules and non-bonded interactions within the single molecule atoms are still computed? The sets of atoms for energy groups and such exclusions are defined by the index groups, not molecules. See manual 7.3 and wherever it talks about groups in an early chapter. On Sun, Apr 17, 2011 at 10:38 PM, Sikandar Mashayak symasha...@gmail.com wrote: Hi When we define energy group exclusions e.g. like in manual energygrp excl = Protein Protein SOL SOL and do md rerun, then only non-bonded interactions between Protein and SOL are computed. I am wondering what happens to bonded interactions within the protein, do they contribute to energies even though we have excluded protein-protein interactions? Bonded interactions are unaffected, as you will see if you try it. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: energy group exclusions
I just did 2 tests in first I do md rerun with SOL SOL exclusions along with PME option then I get forces on water atoms but in second case when I use Cut-Off for electrostatic forces are zero... not sure why PME introduces forces despite using energy exclusion group... On Tue, Apr 19, 2011 at 11:39 AM, Sikandar Mashayak symasha...@gmail.comwrote: Also, in the case of spc/e bulk water when I do md rerun with SOL SOL exlcusion I see forces on water atoms, however I was expecting it to be zero. On Tue, Apr 19, 2011 at 11:12 AM, Sikandar Mashayak symasha...@gmail.comwrote: Yes, 7.3.19 says that all non-nonbonded interactions are excluded within energy_exclusion groups. What I really trying is to get forces on water atoms only because of water water interactions and I want force on protein atoms to be zero, so I do md rerun with energy_exclusion as PROTEIN PROTEIN PROTEIN SOL and also remove any bond interaction information from .top file for protein, but still I get force values on protein atoms. Not sure whats going wrong? thanks sikandar On Tue, Apr 19, 2011 at 12:04 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/19/2011 2:57 PM, Sikandar Mashayak wrote: so that means if I define a index group GRP and energy exclusion GRP GRP then all the non-boned interactions between atoms belonging to GRP group are excluded? What does manual 7.3.19 say? Mark On Mon, Apr 18, 2011 at 7:43 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/18/2011 1:43 PM, Sikandar Mashayak wrote: Also, what about non-bonded interactions within the protein? Does exclusion group only exclude the non-bonded interactions between two different molecules and non-bonded interactions within the single molecule atoms are still computed? The sets of atoms for energy groups and such exclusions are defined by the index groups, not molecules. See manual 7.3 and wherever it talks about groups in an early chapter. On Sun, Apr 17, 2011 at 10:38 PM, Sikandar Mashayak symasha...@gmail.com wrote: Hi When we define energy group exclusions e.g. like in manual energygrp excl = Protein Protein SOL SOL and do md rerun, then only non-bonded interactions between Protein and SOL are computed. I am wondering what happens to bonded interactions within the protein, do they contribute to energies even though we have excluded protein-protein interactions? Bonded interactions are unaffected, as you will see if you try it. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: energy group exclusions
so that means if I define a index group GRP and energy exclusion GRP GRP then all the non-boned interactions between atoms belonging to GRP group are excluded? On Mon, Apr 18, 2011 at 7:43 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/18/2011 1:43 PM, Sikandar Mashayak wrote: Also, what about non-bonded interactions within the protein? Does exclusion group only exclude the non-bonded interactions between two different molecules and non-bonded interactions within the single molecule atoms are still computed? The sets of atoms for energy groups and such exclusions are defined by the index groups, not molecules. See manual 7.3 and wherever it talks about groups in an early chapter. On Sun, Apr 17, 2011 at 10:38 PM, Sikandar Mashayak symasha...@gmail.com wrote: Hi When we define energy group exclusions e.g. like in manual energygrp excl = Protein Protein SOL SOL and do md rerun, then only non-bonded interactions between Protein and SOL are computed. I am wondering what happens to bonded interactions within the protein, do they contribute to energies even though we have excluded protein-protein interactions? Bonded interactions are unaffected, as you will see if you try it. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] forces on water spce due to settle
Hi When water is modeled using SPC/E along with Settle for bond-constraints, then in trajectory file do the forces on water atoms contain any contribution from bond-constraints or only forces due to non-bonded interactions with other water molecule atoms are written? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] energy group exclusions
Hi When we define energy group exclusions e.g. like in manual energygrp excl = Protein Protein SOL SOL and do md rerun, then only non-bonded interactions between Protein and SOL are computed. I am wondering what happens to bonded interactions within the protein, do they contribute to energies even though we have excluded protein-protein interactions? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: energy group exclusions
Also, what about non-bonded interactions within the protein? Does exclusion group only exclude the non-bonded interactions between two different molecules and non-bonded interactions within the single molecule atoms are still computed? On Sun, Apr 17, 2011 at 10:38 PM, Sikandar Mashayak symasha...@gmail.comwrote: Hi When we define energy group exclusions e.g. like in manual energygrp excl = Protein Protein SOL SOL and do md rerun, then only non-bonded interactions between Protein and SOL are computed. I am wondering what happens to bonded interactions within the protein, do they contribute to energies even though we have excluded protein-protein interactions? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Adding Virtual Site to the Molecule
Hi I am thinking of a simulation set up, where I modify a structure/topology of a molecule under consideration, in which, I want to introduce a dummy atom/site which will always be located at center of mass of a molecule and it will only interact with dummy atom of other molecule. I am not sure how to achieve this, will really appreciate any help in this regard. thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Taking difference of forces in two trajectories
Hi I want to test two test potentials compared to reference potential. I have md trajectories from reference potential. So I do mdrun -rerun with two different test potentials and get two separate trajectory files. Now I want to compute difference between forces acting on each atom in each frame due to different test potentials. Is there any way where two trajectories with same position values but different forces can be used to get third .trr file with forces which are difference of first two? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Taking difference of forces in two trajectories
hey thanks for the explanation.. for some constraints I need to have the difference of forces in the .trr format so that I have position,velocity and force error values in one single .trr file. , I dont think g_traj would help me getting that.. is there any other option? On Thu, Mar 31, 2011 at 4:44 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sikandar Mashayak wrote: Hi I want to test two test potentials compared to reference potential. I have md trajectories from reference potential. So I do mdrun -rerun with two different test potentials and get two separate trajectory files. Now I want to compute difference between forces acting on each atom in each frame due to different test potentials. Is there any way where two trajectories with same position values but different forces can be used to get third .trr file with forces which are difference of first two? I don't think you can make mdrun calculate differences in two existing trajectories, but you can extract forces using g_traj and take the difference between the two output files. The file sizes may get extremely large for either long trajectories or many atoms. -Justin thanks sikandar -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] More than one settle type.
Hi I am performing SPC/E water simulation where I want to fix location of one water molecule and let others move. To do that I have defined two groups with name SOL0 and SOL, where SOL0 has just one water molecule and SOL grp contains all others. In .mdp file I define freezegrps as SOL0 . When I do the simulation by mdrun I get error that More than one settle type.. I understand this means, I can not have two molecules with [settle] constraints, I will have define [constraint] for one SPC/E molecule explicitly. Can anyone please suggest me how to do it? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Gromacs Quotes
Hi I am wondering where can I find the file containing all the Gromacs Quotes , which are printed at the end of program run? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] COM removal in Non_Equilibrium MD
Hi If I want to simulate couette flow inside nano-channel, should I be using COM removal option or not? I mean will there be any erroneous COM motion, which needs to be corrected using COM option in .mdp file? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] gromacs 4.5.1 trjcat error
Hi I am trying to concat.. 3 trajectory files of 2ns each. But when I run the command trjact -f 2.trr 4.trr 6.trr -o 246.trr gromacs 4.5.1 gives me following error... File input/output error: Cannot write trajectory frame; maybe you are out of quota? There seems to be lot of free space available on HD, so I am not sure what quota this error is referring to ? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Template file in gromacs4.5.1
Hi I had developed couple of post processing/analysis codes in earlier version of gromacs4.0.7. Now I have upgraded to gromacs4.5.1 and when I check its template file , its completely different that the earlier version. Does that mean old post-processing codes have to rewritten if I were to use new gromacs? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Template file in gromacs4.5.1
Also, will there be any errors if I use trajectory computed by gromacs4.5.1 and use post processing code developed for gromacs4.0.7. I plan to keep both versions of gromacs installed on my system, until I get fully comfortable new version! On Tue, Oct 19, 2010 at 4:14 PM, Sikandar Mashayak symasha...@gmail.comwrote: Hi I had developed couple of post processing/analysis codes in earlier version of gromacs4.0.7. Now I have upgraded to gromacs4.5.1 and when I check its template file , its completely different that the earlier version. Does that mean old post-processing codes have to rewritten if I were to use new gromacs? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs installation problem @ RHEL5.5 server
hey thanks Sander for bringing my attention to -nt option.. ;) -- sikandar On Thu, Oct 14, 2010 at 6:08 AM, Sander Pronk pr...@cbr.su.se wrote: On 14 Oct 2010, at 05:49 , Sikandar Mashayak wrote: Recently I installed gromacs4.5.1 without mpi support on my workstation with 8 cores using cmake and make -j 8, make install commands ( as suggested on installation instructions). Now when I do mdrun it automatically utilizes all the cores and runs much faster than earlier version (4.0.7) , which was not using all cores. I am also surprised , how can mdrun runs on 8 cores without explicitly specifying no. of cores? Its good that mdrun is using all cores, but there may be situations when I dont want mdrun to use all cores. Can I anyone suggest how to control that? use the '-nt' option of mdrun to specify the number of threads. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs installation problem @ RHEL5.5 server
Recently I installed gromacs4.5.1 without mpi support on my workstation with 8 cores using cmake and make -j 8, make install commands ( as suggested on installation instructions). Now when I do mdrun it automatically utilizes all the cores and runs much faster than earlier version (4.0.7) , which was not using all cores. I am also surprised , how can mdrun runs on 8 cores without explicitly specifying no. of cores? Its good that mdrun is using all cores, but there may be situations when I dont want mdrun to use all cores. Can I anyone suggest how to control that? thanks sikandar On Wed, Oct 13, 2010 at 10:35 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 14/10/2010 1:35 PM, Sathish wrote: Thanks for clarifying my doubts. I have started to run demo its working. I have checked processor speed its says only one cpu is running for that program (pdb2gmx). my server configuration (RHEL 5.5) is 2 processor with 6 core, totally 24 processor. I have set export NCPU=24 while installing gromacs. Could you tell me how to run gromacs with all processor ? The only thing that parallelizes is mdrun. Nothing much else runs for long enough for it to be worth it. Either MPI or thread-based parallelism can work. Search the website and/or tutorial material for more details. Mark On Wed, Oct 13, 2010 at 8:24 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sathish wrote: Dear Mark, wow its working. Thank you lot.. As per installation instruction gromacs installed successfully and demo also working. Then i have downloaded test set gmxtest-4.0.4.tgz. While running i got error message like this, [r...@xxx gmxtest]# ./gmxtest.pl http://gmxtest.pl all FAILED. Check files in angles1 FAILED. Check files in angles125 FAILED. Check files in bham FAILED. Check files in bonds1 FAILED. Check files in bonds125 FAILED. Check files in dih1 FAILED. Check files in dih125 FAILED. Check files in g96angles1 FAILED. Check files in g96angles125 FAILED. Check files in g96bonds1 FAILED. Check files in g96bonds125 FAILED. Check files in imp1 FAILED. Check files in imp36 FAILED. Check files in morse FAILED. Check files in rb1 FAILED. Check files in rb125 16 out of 16 simple tests FAILED FAILED. Check files in acetonitrilRF FAILED. Check files in aminoacids FAILED. Check files in argon FAILED. Check files in butane FAILED. Check files in dec+water FAILED. Check files in ethyleenglycol FAILED. Check files in fe_test FAILED. Check files in field FAILED. Check files in nacl FAILED. Check files in sw FAILED. Check files in tip4p FAILED. Check files in tip4pflex FAILED. Check files in urea FAILED. Check files in water 14 out of 14 complex tests FAILED FAILED. Check files in kernel020 FAILED. Check files in kernel120 FAILED. Check files in kernel121 FAILED. Check files in kernel122 FAILED. Check files in kernel123 FAILED. Check files in kernel124 FAILED. Check files in kernel220 FAILED. Check files in kernel221 FAILED. Check files in kernel222 FAILED. Check files in kernel223 FAILED. Check files in kernel224 FAILED. Check files in kernel320 FAILED. Check files in kernel321 FAILED. Check files in kernel322 FAILED. Check files in kernel323 FAILED. Check files in kernel324 16 out of 63 kernel tests FAILED Error not all 45 pdb2gmx tests have been done successfully Only 9 energies in the log file [r...@xxx gmxtest]# Could you explain what is exact problem and how to solve it? 1. The test set is not very robust, so failures are not necessarily indicative of any actual problem. 2. You're using the 4.0.4 test set with version 4.5.1, so some failures are probably due to new command line options, etc. (especially in the case of pdb2gmx) being necessary but not invoked. As it stands, there is no effective way to test the validity of a Gromacs installation. -Justin On Wed, Oct 13, 2010 at 6:15 PM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2010-10-13 10.54, Sathish wrote: Dear Mark, I have one more doubt. How to run luck. If i run luck anywhere its says command not found.. my installed and binary directory cant find luck program. how to do? without checking luck shall i start to run demo? Instructions are outdated. The program is now called g_luck On Wed, Oct 13, 2010 at 3:19 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 13/10/2010 5:01 PM, Mark Abraham wrote: On 13/10/2010 4:55 PM, Sathish wrote: Dear Mark, Thanks for your reply. In my server gromacs installed at local/gromacs. I have checked out point 8 as you mentioned. It was working with this source
[gmx-users] Re: forces from trajectory
Could anyone please clarify on my previous question? I am very confused about the force value issue. thanks sikandar On Thu, Oct 7, 2010 at 2:27 PM, Sikandar Mashayak symasha...@gmail.comwrote: Hi In the post-processing ( analysis) code using gromacs trajectory, I access force values on atom using fr.x[indx_atm][XX]. The confusion I have is that what force is it? is it the force before constraints ( fixed bonds) are applied or is it the effective force due to atom-atom interactions plus any constraints? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] forces from trajectory
Hi In the post-processing ( analysis) code using gromacs trajectory, I access force values on atom using fr.x[indx_atm][XX]. The confusion I have is that what force is it? is it the force before constraints ( fixed bonds) are applied or is it the effective force due to atom-atom interactions plus any constraints? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] tutorial on channel simulations
Hi I want to perform water channel simulations, where channel is connected to bath of bulk water at standard thermodynamic conditions. The objective is to get the density distribution of water inside the channel , which is in equilibrium with the bath. Is there any tutorial specific to gromacs which deals with the simulation I want to perform? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Thermodynamic State of SPC/E bulk water, by genbox
Hi When a bulk SPC/E water box(.gro) is created using the command genbox -cs spc216.gro -box 4.0 4.0 4.0, what is the thermodynamic condition of water? Is it 300K at 1atm? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Thermodynamic State of SPC/E bulk water, by genbox
I am concerned about the number density of water. At T = 300 K and P = 1 atm, SPC/E water has certain number density (no. of molecules/nm^3). With genbox I get .gro file with 34.04 molecules/nm^3 number density, which will remain constant even if I do equilibration in NVT simulation set up. So does that 34.04 molecules/nm^3 corresponds to thermodynamic condition of water at 300K and 1 atm. thanks sikandar On Fri, Jun 18, 2010 at 12:20 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2010-06-18 18.24, Sikandar Mashayak wrote: Hi When a bulk SPC/E water box(.gro) is created using the command genbox -cs spc216.gro -box 4.0 4.0 4.0, what is the thermodynamic condition of water? Is it 300K at 1atm? thanks sikandar No. You have to equilibrate because the box is not completely full. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Running gromacs in parallel on multicore machine
Hi I am wondering whether its possible to run gromacs in parallel on single processor machine with multiple cores? I have 8 core processor, when I run mdrun in serial I see only one of those is used at 100%. I am thinking, if possible, to use all cores approximately equally by running mdrun in parallel and hoping to get results faster. Any suggestions? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Running gromacs in parallel on multicore machine
well I installed the mpi enabled mdrun and execute it with option -np 8, but still I see only core is being used at 100% instead of 8. Is there additional settings to be done to correct this.? thanks sikandar On Tue, Jun 1, 2010 at 4:18 PM, Mark Abraham mark.abra...@anu.edu.auwrote: - Original Message - From: Sikandar Mashayak symasha...@gmail.com Date: Wednesday, June 2, 2010 7:17 Subject: [gmx-users] Running gromacs in parallel on multicore machine To: Discussion list for GROMACS users gmx-users@gromacs.org Hi I am wondering whether its possible to run gromacs in parallel on single processor machine with multiple cores? I have 8 core processor, when I run mdrun in serial I see only one of those is used at 100%. I am thinking, if possible, to use all cores approximately equally by running mdrun in parallel and hoping to get results faster. Any suggestions? Compiling with MPI and running in parallel is your only current option. See GROMACS webpage. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mdrun segmentation fault
Hi I have gromacs input files for md simulation, with these set up files (*.mdp,*.top,*.itp *.gro), I can successfully run grompp and mdrun on one machine, but when I move it to other machine, I get segmentation fault when I do mdrun. Both the machines have exactly same types of installation of gromacs 4.0.7 . Also, I can run water tutorials successfully on both the machines. So what could be the source of segmentation fault? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun segmentation fault
) pp. 8577-8592 --- Thank You --- Using the Ewald3DC correction for systems with a slab geometry. PLEASE READ AND CITE THE FOLLOWING REFERENCE Y. In-Chul and M. L. Berkowitz Ewald summation for systems with slab geometry J. Chem. Phys. 111 (1999) pp. 3155-3162 --- Thank You --- Using a Gaussian width (1/beta) of 0.352179 nm for Ewald Cut-off's: NS: 1.1 Coulomb: 1.1 LJ: 1.1 System total charge: 0.000 Generated table with 4200 data points for Ewald. Tabscale = 2000 points/nm Generated table with 4200 data points for LJ6. Tabscale = 2000 points/nm Generated table with 4200 data points for LJ12. Tabscale = 2000 points/nm Enabling SPC water optimization for 2137 molecules. Configuring nonbonded kernels... Testing ia32 SSE2 support... present. Removing pbc first time PLEASE READ AND CITE THE FOLLOWING REFERENCE S. Miyamoto and P. A. Kollman SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models J. Comp. Chem. 13 (1992) pp. 952-962 --- Thank You --- There are: 7699 Atoms Max number of connections per atom is 2 Total number of connections is 8548 Max number of graph edges per atom is 2 Total number of graph edges is 8548 Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 0.00e+00 Initial temperature: 304.27 K Started mdrun on node 0 Thu May 20 16:33:38 2010 Step Time Lambda 00.00.0 Grid: 5 x 5 x 14 cells Long Range LJ corr.: C6 1.1930e-03 Long Range LJ corr.: Epot -415.301, Pres: -51.4754, Vir:415.301 Energies (kJ/mol) LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 6.44979e+04 -4.15301e+02 -1.00185e+05 -4.94669e+03 -4.10490e+04 Kinetic En. Total Energy Conserved En.Temperature Pressure (bar) 1.72141e+04 -2.38349e+04 -2.38347e+043.22940e+021.36187e+04 On Thu, May 20, 2010 at 4:30 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sikandar Mashayak wrote: Hi I have gromacs input files for md simulation, with these set up files (*.mdp,*.top,*.itp *.gro), I can successfully run grompp and mdrun on one machine, but when I move it to other machine, I get segmentation fault when I do mdrun. Both the machines have exactly same types of installation of gromacs 4.0.7 . Also, I can run water tutorials successfully on both the machines. So what could be the source of segmentation fault? MD is chaotic, so you may not get the same result every time you run a simulation. Since you've not said how quickly the seg fault occurs it is exceptionally hard to diagnose. Generally, seg faults with mdrun occur because the system crashes from an instability. Without substantially more information (system contents, .mdp settings, relevant log file output, etc) there is not much more to suggest. -Justin thanks sikandar -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] water atom locations from genbox
I have to create a box with given number of water molecules (spc/e) in it. So I use genbox -cs spc216.gro -maxsol n -box , with appropriate box size and n. But I observe in the out.gro that some atoms are outside the box, so How do I make genbox to keep all atoms within the box specified? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] water atom locations from genbox
suppose I am not going to use PBC and want all the atoms within the specified boundaries.. On Fri, May 14, 2010 at 1:42 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sikandar Mashayak wrote: I have to create a box with given number of water molecules (spc/e) in it. So I use genbox -cs spc216.gro -maxsol n -box , with appropriate box size and n. But I observe in the out.gro that some atoms are outside the box, so How do I make genbox to keep all atoms within the box specified? If you plan on using periodic boundary conditions, outside is irrelevant... http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin thanks sikandar -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] combine two gro into one
I need to do water channel simulations... I have two gro files with me...one for wall atoms and one for water atoms...assuming the co-ordinates of atoms are appropriate, I just need to rename the indices of each atom appropriately and append one file to anotherI plan to do it by hand...but it will be great if there is an automatic way of doing it in gromacs? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] combine two gro into one
yeah I know its simple, but only concern I have is that, the index of atom/residue in two files may not be in agreement, so I have to change/shift index of atoms in one of the file. but anyway I guess I will have to do it manually thanks sikandar On Thu, May 13, 2010 at 10:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sikandar Mashayak wrote: I need to do water channel simulations... I have two gro files with me...one for wall atoms and one for water atoms...assuming the co-ordinates of atoms are appropriate, I just need to rename the indices of each atom appropriately and append one file to anotherI plan to do it by hand...but it will be great if there is an automatic way of doing it in gromacs? This is a simple task that can be done with the Unix 'cat' command. Thus there is no Gromacs tool that reproduces this function. A few seconds with a text editor after concatenation to remove unnecessary title lines and box vectors and you're done, assuming (as you've said) that all the coordinates are appropriately defined. The whole process probably takes less typing than sending this email :) -Justin thanks sikandar -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Segmentation fault with gromacs executables
Hi I am facing this strange problem of segmentation fault while executing mpi-enabled gromacs executables on remote server. I source GMXRC, so that I can access executables from any directory without specifying full path of gromacs/bin. And when I execute, say grompp, I get segmentation fault. But when I use the same command by specifying full path /home/.../gromacs/bin/grompp , it executes without any issues!! Whats wrong going on here? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Potential Tables for user defined potentials
Hi Gareth Thanks for the notes on user defined potentials in GROMACS. I will go through it and will send you the feedback after I get the simulation results. Thanks sikandar On Sun, Apr 4, 2010 at 11:27 AM, Gareth Tribello gareth.tribe...@gmail.comwrote: Hi all I have just been stuck on this very problem of user defined potentials. When I emailed this list I was asked if I could make notes on the solution as this is a problem that seems to come up a lot. Anyway, I will send the notes to you separately Sikandar and would ask if anyone knows where should put/send them if they are to be accessible to the user community? Many thanks Gareth On Sun, Apr 4, 2010 at 3:47 AM, Justin A. Lemkul jalem...@vt.edu wrote: Sikandar Mashayak wrote: Hi I plan to do 'fluid in channel' simulations using GROMACS 4.0.7. For that I need to use custom potential field parameters for fluid-fluid and fluid-wall interactions. So my question is that, how can I use potential table approach to specify fluid-fluid and fluid-wall interactions seperately? Start with the manual, section 6.7.2, and see the table*.xvg in the /share/top subdirectory of your Gromacs installation for examples. -Justin Thanks sikandar -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Potential Tables for user defined potentials
Hi I plan to do 'fluid in channel' simulations using GROMACS 4.0.7. For that I need to use custom potential field parameters for fluid-fluid and fluid-wall interactions. So my question is that, how can I use potential table approach to specify fluid-fluid and fluid-wall interactions seperately? Thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Parallel vs Serial Gromacs Run Results
Is there any difference between paralley computed GROMACS results and serially computed results? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] CG Force and Potential through do_force()
@ Mark :: you said if the potential is never used then I dont have to worry about storing its value. Suppose I am replacing Coulombic interactions with something of its equivalent through new force field, and I dont store the potential due to it, will I still get the similar results in terms of structure (RDF). Of course I am assuming that new force can accurately replace the Coulombic interactions among the charged atoms. By just having correct forces acting on the atoms and not worrying about storing potential energies, will I still get same trajectory as with storing potential energies. thanks sikandar On Thu, Mar 25, 2010 at 5:45 AM, XAvier Periole x.peri...@rug.nl wrote: If your force is between atom pairs you might be better trying to give all of that as a tabulated potential ... no coding. On Mar 25, 2010, at 7:14 AM, Mark Abraham wrote: - Original Message - From: Sikandar Mashayak symasha...@gmail.com Date: Thursday, March 25, 2010 15:12 Subject: Re: [gmx-users] CG Force and Potential through do_force() To: Discussion list for GROMACS users gmx-users@gromacs.org well if I need to add it by myself, I am not very sure in what variable to add it to. Like I said, I know to add the force on the atom i do f[indxofatom][XX]= forcevalue, where to potential value due to this force? It's not easy. Look at how the generic kernel does it and work you way back through the data structures. Mark On Wed, Mar 24, 2010 at 10:52 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 25/03/2010 2:42 PM, Sikandar Mashayak wrote: Hi I want to do Coarse-Grained simulation in Gromacs. I have one CG force formula, which I plan to implement by adding a short code in do_force() routine in Gromacs 4.0.7 source code. After browsing through the do_force() code, I am now familiar with data structure relevant to add the new force. I mean, I can specify new force by adding to f[indx][XX] and so on. But I am not very sure about potential, whether do I have to explicitly specify the potential on atoms due to this force or gromacs automatically takes care of it by knowing the forces on each atoms? You will need to add that yourself if you want the reported potential to be accurate. GROMACS uses the given parameters in its inner loops to calculate energies and forces. The former are not reverse-engineered from the latter. If the potential is never used, however, then you can forget about it... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] CG Force and Potential through do_force()
@ Xavier :: I am trying out table approach also. But I am facing some issues with it. To start with , as a test run, i use GROMACS provided table6-12.xvg table for LJ interactions. Using this table I am running water bulk simulations. In mdp file I specify to use PME for electrostatics and User for LJ by providing the table6-12.xvg file. But the simulation crashes with the notes ::t = 0.000 ps: Water molecule starting at atom 5363 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates thanks sikandar On Thu, Mar 25, 2010 at 11:26 AM, Sikandar Mashayak symasha...@gmail.comwrote: @ Mark :: you said if the potential is never used then I dont have to worry about storing its value. Suppose I am replacing Coulombic interactions with something of its equivalent through new force field, and I dont store the potential due to it, will I still get the similar results in terms of structure (RDF). Of course I am assuming that new force can accurately replace the Coulombic interactions among the charged atoms. By just having correct forces acting on the atoms and not worrying about storing potential energies, will I still get same trajectory as with storing potential energies. thanks sikandar On Thu, Mar 25, 2010 at 5:45 AM, XAvier Periole x.peri...@rug.nl wrote: If your force is between atom pairs you might be better trying to give all of that as a tabulated potential ... no coding. On Mar 25, 2010, at 7:14 AM, Mark Abraham wrote: - Original Message - From: Sikandar Mashayak symasha...@gmail.com Date: Thursday, March 25, 2010 15:12 Subject: Re: [gmx-users] CG Force and Potential through do_force() To: Discussion list for GROMACS users gmx-users@gromacs.org well if I need to add it by myself, I am not very sure in what variable to add it to. Like I said, I know to add the force on the atom i do f[indxofatom][XX]= forcevalue, where to potential value due to this force? It's not easy. Look at how the generic kernel does it and work you way back through the data structures. Mark On Wed, Mar 24, 2010 at 10:52 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 25/03/2010 2:42 PM, Sikandar Mashayak wrote: Hi I want to do Coarse-Grained simulation in Gromacs. I have one CG force formula, which I plan to implement by adding a short code in do_force() routine in Gromacs 4.0.7 source code. After browsing through the do_force() code, I am now familiar with data structure relevant to add the new force. I mean, I can specify new force by adding to f[indx][XX] and so on. But I am not very sure about potential, whether do I have to explicitly specify the potential on atoms due to this force or gromacs automatically takes care of it by knowing the forces on each atoms? You will need to add that yourself if you want the reported potential to be accurate. GROMACS uses the given parameters in its inner loops to calculate energies and forces. The former are not reverse-engineered from the latter. If the potential is never used, however, then you can forget about it... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org
[gmx-users] CG Force and Potential through do_force()
Hi I want to do Coarse-Grained simulation in Gromacs. I have one CG force formula, which I plan to implement by adding a short code in do_force() routine in Gromacs 4.0.7 source code. After browsing through the do_force() code, I am now familiar with data structure relevant to add the new force. I mean, I can specify new force by adding to f[indx][XX] and so on. But I am not very sure about potential, whether do I have to explicitly specify the potential on atoms due to this force or gromacs automatically takes care of it by knowing the forces on each atoms? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] CG Force and Potential through do_force()
well if I need to add it by myself, I am not very sure in what variable to add it to. Like I said, I know to add the force on the atom i do f[indxofatom][XX]= forcevalue, where to potential value due to this force? thanks sikandar On Wed, Mar 24, 2010 at 10:52 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 25/03/2010 2:42 PM, Sikandar Mashayak wrote: Hi I want to do Coarse-Grained simulation in Gromacs. I have one CG force formula, which I plan to implement by adding a short code in do_force() routine in Gromacs 4.0.7 source code. After browsing through the do_force() code, I am now familiar with data structure relevant to add the new force. I mean, I can specify new force by adding to f[indx][XX] and so on. But I am not very sure about potential, whether do I have to explicitly specify the potential on atoms due to this force or gromacs automatically takes care of it by knowing the forces on each atoms? You will need to add that yourself if you want the reported potential to be accurate. GROMACS uses the given parameters in its inner loops to calculate energies and forces. The former are not reverse-engineered from the latter. If the potential is never used, however, then you can forget about it... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
