Re: [gmx-users] g_saltbr speed
Dear users, Its the continuation of the question I asked yesterday, Inorder to reduce the memory usage during g_saltbr calculations i got the trajectory of only protein, and tpr file without water and was able to successfully run it. But unfortunately this again got stopped at 36ns as it had stopped when i was using the whole trajectory. I tried with -dt 2, still the same problem exists. Kindly suggest a way out of this situation. Thank you With Regards Kavya On Thu, Jul 12, 2012 at 6:11 PM, Kavyashree M hmkv...@gmail.com wrote: Dear Sir, Thank you It worked :). a very usefull suggestion. But it did not promt to choose any option. I used index file. Thank you Kavya On Thu, Jul 12, 2012 at 6:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 7/12/12 8:31 AM, Kavyashree M wrote: Ok may be i need to specify an index file. I will try that. And regarding the WARNING: this .tpx file is not fully functional. I hope it will work fine enough to finish g_saltbr calculation? In principle, you should be prompted to choose a default group, but you can also use a custom index group as needed. The warning message is intended to note that the .tpr file you produce will not likely work for running an actual simulation. It should be fine for analysis. -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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] g_saltbr speed
On 7/13/12 11:50 AM, Kavyashree M wrote: Dear users, Its the continuation of the question I asked yesterday, Inorder to reduce the memory usage during g_saltbr calculations i got the trajectory of only protein, and tpr file without water and was able to successfully run it. But unfortunately this again got stopped at 36ns as it had stopped when i was using the whole trajectory. I tried with -dt 2, still the same problem exists. Kindly suggest a way out of this situation. How long is the trajectory? How many frames? What is the size of the file on disk? It sounds to me like you're simply exhausting available memory, so the only advice is in the link I posted before - use fewer frames or use a machine that has more memory to do the analysis. -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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] g_saltbr speed
Its 50ns 25000 frames. the xtc file is 695MB. it has 16GB RAM. So will that be insufficient? I have previously run other analysis which used to take huge memory, for eg. covariance analysis, in a system with much lesser memory even though CPU usage was low the job used to finish. But in this case its not so. Thank you kavya On Fri, Jul 13, 2012 at 9:22 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 7/13/12 11:50 AM, Kavyashree M wrote: Dear users, Its the continuation of the question I asked yesterday, Inorder to reduce the memory usage during g_saltbr calculations i got the trajectory of only protein, and tpr file without water and was able to successfully run it. But unfortunately this again got stopped at 36ns as it had stopped when i was using the whole trajectory. I tried with -dt 2, still the same problem exists. Kindly suggest a way out of this situation. How long is the trajectory? How many frames? What is the size of the file on disk? It sounds to me like you're simply exhausting available memory, so the only advice is in the link I posted before - use fewer frames or use a machine that has more memory to do the analysis. -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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] g_saltbr speed
On 7/13/12 12:05 PM, Kavyashree M wrote: Its 50ns 25000 frames. the xtc file is 695MB. it has 16GB RAM. So will that be insufficient? I have previously run other analysis which used to take huge memory, for eg. covariance analysis, in a system with much lesser memory even though CPU usage was low the job used to finish. But in this case its not so. I can't see a reason why the file itself would present a problem. I have run g_saltbr on similarly sized systems. Sorry, I can't offer an explanation as to why it's stopping prematurely. -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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] g_saltbr speed
Ok... I will try other options. Thanks Kavya On Fri, Jul 13, 2012 at 10:23 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 7/13/12 12:05 PM, Kavyashree M wrote: Its 50ns 25000 frames. the xtc file is 695MB. it has 16GB RAM. So will that be insufficient? I have previously run other analysis which used to take huge memory, for eg. covariance analysis, in a system with much lesser memory even though CPU usage was low the job used to finish. But in this case its not so. I can't see a reason why the file itself would present a problem. I have run g_saltbr on similarly sized systems. Sorry, I can't offer an explanation as to why it's stopping prematurely. -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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] g_saltbr speed
On 7/12/12 4:51 AM, Kavyashree M wrote: Dear Gromacs users, I was running the saltbridge calculations for a dimeric protein simulation using g_saltbr, But its taking very long time, almost four days still its not completed. Could anyone has suggestion regarding this issue? I am using the same system - Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz where i ran MD. Please give some suggestion as to how to increase the speed of calculation. Command i issued was: g_saltbr -f ../traj.xtc -s md.tpr -t 0.4 -sep g_saltbr calculates properties of all possible ionic pairs in the system, so if there are many, the calculation might take a long time. Four days sounds ridiculous, and perhaps the program has frozen by exhausting the available memory. -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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] g_saltbr speed
Dear Sir, That is true as the number of the frames increased the memory had almost reached 95% but still it has been in 95% since long and CPU usage drops down to 1.5 -2 % but in many cases i have seen that still it will run (off course slowly) and finish. But this was too long. So any suggestions? Thank you Kavya On Thu, Jul 12, 2012 at 3:39 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 7/12/12 4:51 AM, Kavyashree M wrote: Dear Gromacs users, I was running the saltbridge calculations for a dimeric protein simulation using g_saltbr, But its taking very long time, almost four days still its not completed. Could anyone has suggestion regarding this issue? I am using the same system - Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz where i ran MD. Please give some suggestion as to how to increase the speed of calculation. Command i issued was: g_saltbr -f ../traj.xtc -s md.tpr -t 0.4 -sep g_saltbr calculates properties of all possible ionic pairs in the system, so if there are many, the calculation might take a long time. Four days sounds ridiculous, and perhaps the program has frozen by exhausting the available memory. -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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] g_saltbr speed
On 7/12/12 6:38 AM, Kavyashree M wrote: Dear Sir, That is true as the number of the frames increased the memory had almost reached 95% but still it has been in 95% since long and CPU usage drops down to 1.5 -2 % but in many cases i have seen that still it will run (off course slowly) and finish. But this was too long. So any suggestions? http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume -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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] g_saltbr speed
Thanks :). will check whether it makes it faster. On Thu, Jul 12, 2012 at 4:27 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 7/12/12 6:38 AM, Kavyashree M wrote: Dear Sir, That is true as the number of the frames increased the memory had almost reached 95% but still it has been in 95% since long and CPU usage drops down to 1.5 -2 % but in many cases i have seen that still it will run (off course slowly) and finish. But this was too long. So any suggestions? http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume -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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] g_saltbr speed
Dear Sir, I had a problem again during g_saltbr calculation it needs .xtc and .tpr file, I can reduce the .xtc file to have only protein but .tpr file will have water also in it. inorder to generate new tpr file without water using grompp, i need topology file without water .. so do you suggest me to go this way.. it appears quite complicated! Thank you Kavya On Thu, Jul 12, 2012 at 4:52 PM, Kavyashree M hmkv...@gmail.com wrote: Thanks :). will check whether it makes it faster. On Thu, Jul 12, 2012 at 4:27 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 7/12/12 6:38 AM, Kavyashree M wrote: Dear Sir, That is true as the number of the frames increased the memory had almost reached 95% but still it has been in 95% since long and CPU usage drops down to 1.5 -2 % but in many cases i have seen that still it will run (off course slowly) and finish. But this was too long. So any suggestions? http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume -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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] g_saltbr speed
On 7/12/12 8:15 AM, Kavyashree M wrote: Dear Sir, I had a problem again during g_saltbr calculation it needs .xtc and .tpr file, I can reduce the .xtc file to have only protein but .tpr file will have water also in it. inorder to generate new tpr file without water using grompp, i need topology file without water .. so do you suggest me to go this way.. it appears quite complicated! In fact, it's quite easy with tpbconv. From tpbconv -h: 3. by creating a .tpx file for a subset of your original tpx file, which is useful when you want to remove the solvent from your .tpx file, or when you want to make e.g. a pure Calpha .tpx file. Note that you may need to use -nsteps -1 (or similar) to get this to work. WARNING: this .tpx file is not fully functional. -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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] g_saltbr speed
I read that. but while executing tpbconv i did not see where i can specify that i do not want solvent? Thanks Kavya On Thu, Jul 12, 2012 at 5:47 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 7/12/12 8:15 AM, Kavyashree M wrote: Dear Sir, I had a problem again during g_saltbr calculation it needs .xtc and .tpr file, I can reduce the .xtc file to have only protein but .tpr file will have water also in it. inorder to generate new tpr file without water using grompp, i need topology file without water .. so do you suggest me to go this way.. it appears quite complicated! In fact, it's quite easy with tpbconv. From tpbconv -h: 3. by creating a .tpx file for a subset of your original tpx file, which is useful when you want to remove the solvent from your .tpx file, or when you want to make e.g. a pure Calpha .tpx file. Note that you may need to use -nsteps -1 (or similar) to get this to work. WARNING: this .tpx file is not fully functional. -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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] g_saltbr speed
Ok may be i need to specify an index file. I will try that. And regarding the WARNING: this .tpx file is not fully functional. I hope it will work fine enough to finish g_saltbr calculation? Thanks Kavya On Thu, Jul 12, 2012 at 5:59 PM, Kavyashree M hmkv...@gmail.com wrote: I read that. but while executing tpbconv i did not see where i can specify that i do not want solvent? Thanks Kavya On Thu, Jul 12, 2012 at 5:47 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 7/12/12 8:15 AM, Kavyashree M wrote: Dear Sir, I had a problem again during g_saltbr calculation it needs .xtc and .tpr file, I can reduce the .xtc file to have only protein but .tpr file will have water also in it. inorder to generate new tpr file without water using grompp, i need topology file without water .. so do you suggest me to go this way.. it appears quite complicated! In fact, it's quite easy with tpbconv. From tpbconv -h: 3. by creating a .tpx file for a subset of your original tpx file, which is useful when you want to remove the solvent from your .tpx file, or when you want to make e.g. a pure Calpha .tpx file. Note that you may need to use -nsteps -1 (or similar) to get this to work. WARNING: this .tpx file is not fully functional. -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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] g_saltbr speed
On 7/12/12 8:31 AM, Kavyashree M wrote: Ok may be i need to specify an index file. I will try that. And regarding the WARNING: this .tpx file is not fully functional. I hope it will work fine enough to finish g_saltbr calculation? In principle, you should be prompted to choose a default group, but you can also use a custom index group as needed. The warning message is intended to note that the .tpr file you produce will not likely work for running an actual simulation. It should be fine for analysis. -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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] g_saltbr speed
Dear Sir, Thank you It worked :). a very usefull suggestion. But it did not promt to choose any option. I used index file. Thank you Kavya On Thu, Jul 12, 2012 at 6:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 7/12/12 8:31 AM, Kavyashree M wrote: Ok may be i need to specify an index file. I will try that. And regarding the WARNING: this .tpx file is not fully functional. I hope it will work fine enough to finish g_saltbr calculation? In principle, you should be prompted to choose a default group, but you can also use a custom index group as needed. The warning message is intended to note that the .tpr file you produce will not likely work for running an actual simulation. It should be fine for analysis. -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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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
