Re: [gmx-users] Speeding up simulation
On 17/08/10 22:36, Justin A. Lemkul wrote: There is no way to limit PME to certain ranges. It is a method for solving infinite sums. Usually PME is a poor choice for in vacuo simulations and the like, since there's nothing to be done for most of the simulation box. This interests me -I've used simple cut-off for in vacuo tests, but I still hadn't made my mind on what electrostatic model I should truly use. Do you have any suggestion? thanks, M. You may want to see how others (in the literature) deal with droplet-type simulations. -Justin Thanks for your help. Sapna On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: sapna sarupria wrote: Hi all, I am running (NVT) simulations of a drop of water (~5 nm in radius) in a big box (~25 nm) in a box and find that the simulations are rather slow. I am getting about 0.8 ns per day when a simulation of bulk system of equivalent number of waters will be much faster. The number of waters is ~12000. I was wondering if anyone can suggest methods with which I can speed up the simulations. I am using domain decomposition and optimize_fft is set to yes. PME is used for the electrostatics. I would suspect that the lag comes from a lot of unused PME calculations. During your run, PME grid points will be assigned to vacuum space, for which nothing needs to be done. You can check imbalances and performance loss in the log file. -Justin Thank you Sincerely Sapna -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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/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/mailing_lists/users.php -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- 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] Speeding up simulation
That might actually be the best approach speed wise. But it depends on what level of accuracy you wish for your calculations. What is your system like? May be you can have a large cut off but you will have to see what the trade off between speed and accuracy is. On Wed, Aug 18, 2010 at 10:26 AM, ms deviceran...@gmail.com wrote: On 17/08/10 22:36, Justin A. Lemkul wrote: There is no way to limit PME to certain ranges. It is a method for solving infinite sums. Usually PME is a poor choice for in vacuo simulations and the like, since there's nothing to be done for most of the simulation box. This interests me -I've used simple cut-off for in vacuo tests, but I still hadn't made my mind on what electrostatic model I should truly use. Do you have any suggestion? thanks, M. You may want to see how others (in the literature) deal with droplet-type simulations. -Justin Thanks for your help. Sapna On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: sapna sarupria wrote: Hi all, I am running (NVT) simulations of a drop of water (~5 nm in radius) in a big box (~25 nm) in a box and find that the simulations are rather slow. I am getting about 0.8 ns per day when a simulation of bulk system of equivalent number of waters will be much faster. The number of waters is ~12000. I was wondering if anyone can suggest methods with which I can speed up the simulations. I am using domain decomposition and optimize_fft is set to yes. PME is used for the electrostatics. I would suspect that the lag comes from a lot of unused PME calculations. During your run, PME grid points will be assigned to vacuum space, for which nothing needs to be done. You can check imbalances and performance loss in the log file. -Justin Thank you Sincerely Sapna -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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/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/mailing_lists/users.php -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- 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 -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- 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] Speeding up simulation
Large cut-offs can bring artificial artifacts. e.g. *Chemical Physics Letters*http://www.sciencedirect.com/science/journal/00092614 Volume 406, Issues 1-3http://www.sciencedirect.com/science?_ob=PublicationURL_tockey=%23TOC%235231%232005%23995939998%23591997%23FLA%23_cdi=5231_pubType=Jview=c_auth=y_acct=C62818_version=1_urlVersion=0_userid=6325866md5=51f91ba17c3ce282da206786a17d50d5, 23 April 2005, Pages 49-53 -Gaurav On Wed, Aug 18, 2010 at 12:04 PM, sapna sarupria sapna.sarup...@gmail.comwrote: That might actually be the best approach speed wise. But it depends on what level of accuracy you wish for your calculations. What is your system like? May be you can have a large cut off but you will have to see what the trade off between speed and accuracy is. On Wed, Aug 18, 2010 at 10:26 AM, ms deviceran...@gmail.com wrote: On 17/08/10 22:36, Justin A. Lemkul wrote: There is no way to limit PME to certain ranges. It is a method for solving infinite sums. Usually PME is a poor choice for in vacuo simulations and the like, since there's nothing to be done for most of the simulation box. This interests me -I've used simple cut-off for in vacuo tests, but I still hadn't made my mind on what electrostatic model I should truly use. Do you have any suggestion? thanks, M. You may want to see how others (in the literature) deal with droplet-type simulations. -Justin Thanks for your help. Sapna On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: sapna sarupria wrote: Hi all, I am running (NVT) simulations of a drop of water (~5 nm in radius) in a big box (~25 nm) in a box and find that the simulations are rather slow. I am getting about 0.8 ns per day when a simulation of bulk system of equivalent number of waters will be much faster. The number of waters is ~12000. I was wondering if anyone can suggest methods with which I can speed up the simulations. I am using domain decomposition and optimize_fft is set to yes. PME is used for the electrostatics. I would suspect that the lag comes from a lot of unused PME calculations. During your run, PME grid points will be assigned to vacuum space, for which nothing needs to be done. You can check imbalances and performance loss in the log file. -Justin Thank you Sincerely Sapna -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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/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/mailing_lists/users.php -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- 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 -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- 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
Re: [gmx-users] Speeding up simulation
sapna sarupria wrote: Hi all, I am running (NVT) simulations of a drop of water (~5 nm in radius) in a big box (~25 nm) in a box and find that the simulations are rather slow. I am getting about 0.8 ns per day when a simulation of bulk system of equivalent number of waters will be much faster. The number of waters is ~12000. I was wondering if anyone can suggest methods with which I can speed up the simulations. I am using domain decomposition and optimize_fft is set to yes. PME is used for the electrostatics. I would suspect that the lag comes from a lot of unused PME calculations. During your run, PME grid points will be assigned to vacuum space, for which nothing needs to be done. You can check imbalances and performance loss in the log file. -Justin Thank you Sincerely Sapna -- 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
Re: [gmx-users] Speeding up simulation
Hi Justin Thanks for your response. I suspect that it is the same thing. Is there a way to make gromacs use PME only within a certain region of the simulation box? Also, how does one know how to fix the load imbalances (in this context)? Thanks for your help. Sapna On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul jalem...@vt.edu wrote: sapna sarupria wrote: Hi all, I am running (NVT) simulations of a drop of water (~5 nm in radius) in a big box (~25 nm) in a box and find that the simulations are rather slow. I am getting about 0.8 ns per day when a simulation of bulk system of equivalent number of waters will be much faster. The number of waters is ~12000. I was wondering if anyone can suggest methods with which I can speed up the simulations. I am using domain decomposition and optimize_fft is set to yes. PME is used for the electrostatics. I would suspect that the lag comes from a lot of unused PME calculations. During your run, PME grid points will be assigned to vacuum space, for which nothing needs to be done. You can check imbalances and performance loss in the log file. -Justin Thank you Sincerely Sapna -- 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 -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- 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] Speeding up simulation
sapna sarupria wrote: Hi Justin Thanks for your response. I suspect that it is the same thing. Is there a way to make gromacs use PME only within a certain region of the simulation box? Also, how does one know how to fix the load imbalances (in this context)? There is no way to limit PME to certain ranges. It is a method for solving infinite sums. Usually PME is a poor choice for in vacuo simulations and the like, since there's nothing to be done for most of the simulation box. You may want to see how others (in the literature) deal with droplet-type simulations. -Justin Thanks for your help. Sapna On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: sapna sarupria wrote: Hi all, I am running (NVT) simulations of a drop of water (~5 nm in radius) in a big box (~25 nm) in a box and find that the simulations are rather slow. I am getting about 0.8 ns per day when a simulation of bulk system of equivalent number of waters will be much faster. The number of waters is ~12000. I was wondering if anyone can suggest methods with which I can speed up the simulations. I am using domain decomposition and optimize_fft is set to yes. PME is used for the electrostatics. I would suspect that the lag comes from a lot of unused PME calculations. During your run, PME grid points will be assigned to vacuum space, for which nothing needs to be done. You can check imbalances and performance loss in the log file. -Justin Thank you Sincerely Sapna -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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/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/mailing_lists/users.php -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- 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
Re: [gmx-users] Speeding up simulation
Hi Justin Thanks for your input. I guess I will do some more literature search and try to optimize the simulations as much as I can. Thanks, Sapna On Tue, Aug 17, 2010 at 5:36 PM, Justin A. Lemkul jalem...@vt.edu wrote: sapna sarupria wrote: Hi Justin Thanks for your response. I suspect that it is the same thing. Is there a way to make gromacs use PME only within a certain region of the simulation box? Also, how does one know how to fix the load imbalances (in this context)? There is no way to limit PME to certain ranges. It is a method for solving infinite sums. Usually PME is a poor choice for in vacuo simulations and the like, since there's nothing to be done for most of the simulation box. You may want to see how others (in the literature) deal with droplet-type simulations. -Justin Thanks for your help. Sapna On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: sapna sarupria wrote: Hi all, I am running (NVT) simulations of a drop of water (~5 nm in radius) in a big box (~25 nm) in a box and find that the simulations are rather slow. I am getting about 0.8 ns per day when a simulation of bulk system of equivalent number of waters will be much faster. The number of waters is ~12000. I was wondering if anyone can suggest methods with which I can speed up the simulations. I am using domain decomposition and optimize_fft is set to yes. PME is used for the electrostatics. I would suspect that the lag comes from a lot of unused PME calculations. During your run, PME grid points will be assigned to vacuum space, for which nothing needs to be done. You can check imbalances and performance loss in the log file. -Justin Thank you Sincerely Sapna -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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/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/mailing_lists/users.php -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- 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 -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- 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] Speeding up simulation
Sapna, Is there a particular reason you're using a box so much larger than the droplet diameter? If your only concern is that periodic images should not see each-other maybe you can use a box length=droplet diameter+2*largest cut-off in the system. Also using a more spherical box shape such as rhombic dodecahedron or the truncated octahedron will help you in reducing the volume of unfilled space. -Gaurav On Tue, Aug 17, 2010 at 5:40 PM, sapna sarupria sapna.sarup...@gmail.comwrote: Hi Justin Thanks for your input. I guess I will do some more literature search and try to optimize the simulations as much as I can. Thanks, Sapna On Tue, Aug 17, 2010 at 5:36 PM, Justin A. Lemkul jalem...@vt.edu wrote: sapna sarupria wrote: Hi Justin Thanks for your response. I suspect that it is the same thing. Is there a way to make gromacs use PME only within a certain region of the simulation box? Also, how does one know how to fix the load imbalances (in this context)? There is no way to limit PME to certain ranges. It is a method for solving infinite sums. Usually PME is a poor choice for in vacuo simulations and the like, since there's nothing to be done for most of the simulation box. You may want to see how others (in the literature) deal with droplet-type simulations. -Justin Thanks for your help. Sapna On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: sapna sarupria wrote: Hi all, I am running (NVT) simulations of a drop of water (~5 nm in radius) in a big box (~25 nm) in a box and find that the simulations are rather slow. I am getting about 0.8 ns per day when a simulation of bulk system of equivalent number of waters will be much faster. The number of waters is ~12000. I was wondering if anyone can suggest methods with which I can speed up the simulations. I am using domain decomposition and optimize_fft is set to yes. PME is used for the electrostatics. I would suspect that the lag comes from a lot of unused PME calculations. During your run, PME grid points will be assigned to vacuum space, for which nothing needs to be done. You can check imbalances and performance loss in the log file. -Justin Thank you Sincerely Sapna -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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/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/mailing_lists/users.php -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- 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 -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- 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
