[gmx-users] table-extension in mdp ?!
Dear users, Please help me with the following problem. My simulation is crashing for an unstability reason I guess. Can you please help me what wrong is exaclty. I had done the simulation with exactly the same input files but with version 4.0.7 and never got this error. Thanks for your comments. Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'solute' Velocities were taken from a Maxwell distribution at 300 K Number of degrees of freedom in T-Coupling group System is 8685.00 NOTE 1 [file md.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file md.mdp]: The sum of the two largest charge group radii (0.204120) is larger than rlist (1.10) - rvdw (1.00) Analysing residue names: There are: 240 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Largest charge group radii for Van der Waals: 0.102, 0.102 nm This run will generate roughly 343 Mb of data output.mdrun step 7200, will finish Tue Jan 18 03:51:24 2011imb F 9% step 7300, will finish Tue Jan 18 03:44:57 2011Warning: 1-4 interaction between 2121 and 2128 at distance 12.290 which is larger than the 1-4 table size 2.100 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size -- 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] table-extension in mdp ?!
On January 17, 2011 at 4:32 PM jojo J joojoojo...@gmail.com wrote: Dear users, Please help me with the following problem. My simulation is crashing for an unstability reason I guess. Can you please help me what wrong is exaclty. I had done the simulation with exactly the same input files but with version 4.0.7 and never got this error. Thanks for your comments. Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours molecule type solute Velocities were taken from a Maxwell distribution at 300 K Number of degrees of freedom in T-Coupling group System is 8685.00 NOTE 1 [file md.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file md.mdp]: The sum of the two largest charge group radii (0.204120) is larger than rlist (1.10) - rvdw (1.00) Analysing residue names: There are: 240 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Largest charge group radii for Van der Waals: 0.102, 0.102 nm This run will generate roughly 343 Mb of data output.mdrun step 7200, will finish Tue Jan 18 03:51:24 2011imb F 9% step 7300, will finish Tue Jan 18 03:44:57 2011Warning: 1-4 interaction between 2121 and 2128 at distance 12.290 which is larger than the 1-4 table size 2.100 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size I seem to have a similar problem but you are having many more than I. If I were you I would fix the two NOTES first. Once those go away the 1-4 interaction warning might disappear as well. TJ Mustard Email: musta...@onid.orst.edu -- 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] table extension
Thanks Mark. I am simulating a dimer in vacuum, and it is my understanding that once a non-bonded interaction has exceeded the table-extension cutoff this interaction will NOT be included in the potential for the remaining simulation, even if it will later come back to a distance within the table-extension. Your answer helped me. It is now a matter of choosing the box dimensions table extension that will be reasonable yet not increase the computation time too much. --Omer. Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Wed, Aug 26, 2009 at 16:03, Mark Abraham mark.abra...@anu.edu.au wrote: Probably not... if you're asking this question because you suspect something's not working properly, you might get enlightenment/a fix quicker if you're more explicit :-) 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
RE: [gmx-users] table extension
Hi, No, this is not correct. A interaction beyond the cut-off + table-extension will get a random energy and force depending on what is stored in the memory of your computer beyond the table___ 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] table extension
Thanks. And what happens if later on it comes back to the cut-off + table-extension range? Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Thu, Aug 27, 2009 at 11:13, Berk Hess g...@hotmail.com wrote: A interaction beyond the cut-off + table-extension will get a random energy and force depending on what is stored in the memory of your computer beyond the table ___ 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] table extension
Omer Markovitch wrote: Thanks. And what happens if later on it comes back to the cut-off + table-extension range? It would look up a non-random energy and force. If the code never noticed the distance was out-of-range, it won't notice it come back into range either. Mark Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Thu, Aug 27, 2009 at 11:13, Berk Hess g...@hotmail.com wrote: A interaction beyond the cut-off + table-extension will get a random energy and force depending on what is stored in the memory of your computer beyond the table ___ 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] table extension
But what if the gmx code did notice it? Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Thu, Aug 27, 2009 at 16:21, Mark Abraham mark.abra...@anu.edu.au wrote: It would look up a non-random energy and force. If the code never noticed the distance was out-of-range, it won't notice it come back into range either. ___ 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] table extension
There is a misunderstanding here about noticing. For efficiency reasons, the code does not check if atoms are beyond the table length. So the code does not care about or notice anything. However, you do care, since you do not want random forces. (Although in nearly all cases the force will be, or zero: fine, no artifacts, or 10^30: immediate crash of mdrun). Berk Date: Thu, 27 Aug 2009 17:18:13 +0300 Subject: Re: [gmx-users] table extension From: omer...@gmail.com To: gmx-users@gromacs.org But what if the gmx code did notice it? Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Thu, Aug 27, 2009 at 16:21, Mark Abraham mark.abra...@anu.edu.au wrote: It would look up a non-random energy and force. If the code never noticed the distance was out-of-range, it won't notice it come back into range either. _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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] table extension
Dear GMXs, I would like to clear something out, for myself: The table extension given in MDP file applies to nonbond_params pairs interactions which are specified in the TOP file (and also electrostatics)? Is there an interaction which does not use the table extension (other then bonds, angles dihdrals)? I have read the manual. Thanks, Omer. ___ 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] table extension
Omer Markovitch wrote: Dear GMXs, I would like to clear something out, for myself: The table extension given in MDP file applies to nonbond_params pairs interactions which are specified in the TOP file (and also electrostatics)? From 7.3.12, yes. These are the nonbonded interactions. Is there an interaction which does not use the table extension (other then bonds, angles dihdrals)? Probably not... if you're asking this question because you suspect something's not working properly, you might get enlightenment/a fix quicker if you're more explicit :-) 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] table-extension
*hi ! I am getting this error with regard to table extensions. Any suggestions to overcome this would be greatly appreciated! Thanks Jayant James * Warning: 1-4 interaction between 429 and 434 at distance 1.002 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file On Fri, Mar 28, 2008 at 11:42 AM, Yang Ye [EMAIL PROTECTED] wrote: jayant james wrote: *hi! I am attempting to run a distance position restrained simulation in water. The **distance and position restraining files are called from the *.top file as posres.itp and disres.itp. After a 200ps run I do not see the distance nor position restraining kicking in. I am not sure if I have specified every thing correctly. I have pasted essential parts of the topology file, em.mdp, pr.mdp, disres.itp and posres.itp. Awaiting your feedback Thanks Jayant James * *TOP FILE* ; Include Position restraint file #ifdef POSRES ;include posre.itp #endif ;includedisres.itp Putting semicolon in front of the line effectively turns off that line. Regards, Yang Ye ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) Residence -24935864, cell-9841042164 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] table-extension
*hi ! I am getting this error with regard to table extensions. Any suggestions to overcome this would be greatly appreciated! Thanks Jayant James * Warning: 1-4 interaction between 429 and 434 at distance 1.002 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file So have a look at the trajectory to see what's exploding, especially in the region of these atoms. Probably you will need to set up your system more carefully, with better EM, and/or equilibration protocols. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
