[gmx-users] 1-4 interaction between atoms in PBC mode
Hi Mark, Yes, I have had success running many GROMACS simulations with a simple graphene sheet inside a box. I believe I have regenerated the .tpr file from the new .mdp as the very first command I issue is: grompp -np $NUM_PROCS -f em.mdp -c $GRO_FILE -p $TOP_FILE -o emtopol.tpr -n index.ndx Please advise me on what I may be doing wrong. Also, note that there appears to be no reference to the statement periodic_molecules = yes in the GROMACS manual as I did a search in the manual for periodic_molecules and the search came back empty. Thanks. Darrell Date: Tue, 22 Sep 2009 15:07:03 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4ab85b77.10...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Hi Mark, I did not have the statement periodic_molecules = yes in the .mdp files. I only had the statement pbc=xyz in the .mdp files. So, I added the periodic_molecules = yes statement to the .mdp files and ran the simulation again. However, this did not appear to resolve the problem as I received the same warning. Well that's a pretty basic requirement that you needed to satisfy. Obviously you also need to re-generate your .tpr from the new .mdp. That'd be the most likely reason for an *identical* output. Have you done enough background reading (e.g. wiki page on Carbon Nanotube simulations) and/or gotten some experience with normal GROMACS simulations? Mark Date: Mon, 21 Sep 2009 16:56:48 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4ab723b0.6040...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Dear GROMACS-ians, I have created an infinite graphene sheet and upon running grompp, I get the following response: /Warning: 1-4 interaction between 10085 and 10445 at distance 19.679 which is larger than the 1-4 table size 1.000 nm Warning: 1-4 interaction between 9244 and 9963 at distance 19.553 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 These are ignored for the rest of the simulation/ I assume that atoms from opposite ends of the simulation box are being seen by GROMACS as being 1-4 neighbors as a result of the PBC, but the shortest distance between the atoms is not being observed. Is this the problem? Is this problem resulting in the system exploding? And, how do I resolve this problem? Did you use periodic_molecules = yes in your .mdp file? 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] 1-4 interaction between atoms in PBC mode
Darrell Koskinen wrote: Hi Mark, Yes, I have had success running many GROMACS simulations with a simple graphene sheet inside a box. I believe I have regenerated the .tpr file from the new .mdp as the very first command I issue is: grompp -np $NUM_PROCS -f em.mdp -c $GRO_FILE -p $TOP_FILE -o emtopol.tpr -n index.ndx Please advise me on what I may be doing wrong. Also, note that there appears to be no reference to the statement periodic_molecules = yes in the GROMACS manual as I did a search in the manual for periodic_molecules and the search came back empty. One error was not mentioning your GROMACS version. :-) Your grompp command line above is for some 3.x version, not some 4.x version. periodic_molecules is a 4.x feature (but mentioned only in section 7.3 IIRC). I've no idea how to solve your problem for 3.x, but if you can reasonably upgrade, you should. Mark Thanks. Darrell Date: Tue, 22 Sep 2009 15:07:03 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4ab85b77.10...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Hi Mark, I did not have the statement periodic_molecules = yes in the .mdp files. I only had the statement pbc=xyz in the .mdp files. So, I added the periodic_molecules = yes statement to the .mdp files and ran the simulation again. However, this did not appear to resolve the problem as I received the same warning. Well that's a pretty basic requirement that you needed to satisfy. Obviously you also need to re-generate your .tpr from the new .mdp. That'd be the most likely reason for an *identical* output. Have you done enough background reading (e.g. wiki page on Carbon Nanotube simulations) and/or gotten some experience with normal GROMACS simulations? Mark Date: Mon, 21 Sep 2009 16:56:48 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4ab723b0.6040...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Dear GROMACS-ians, I have created an infinite graphene sheet and upon running grompp, I get the following response: /Warning: 1-4 interaction between 10085 and 10445 at distance 19.679 which is larger than the 1-4 table size 1.000 nm Warning: 1-4 interaction between 9244 and 9963 at distance 19.553 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 These are ignored for the rest of the simulation/ I assume that atoms from opposite ends of the simulation box are being seen by GROMACS as being 1-4 neighbors as a result of the PBC, but the shortest distance between the atoms is not being observed. Is this the problem? Is this problem resulting in the system exploding? And, how do I resolve this problem? Did you use periodic_molecules = yes in your .mdp file? 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
Re: [gmx-users] 1-4 interaction between atoms in PBC mode
Mark Abraham wrote: Darrell Koskinen wrote: Hi Mark, Yes, I have had success running many GROMACS simulations with a simple graphene sheet inside a box. I believe I have regenerated the .tpr file from the new .mdp as the very first command I issue is: grompp -np $NUM_PROCS -f em.mdp -c $GRO_FILE -p $TOP_FILE -o emtopol.tpr -n index.ndx Please advise me on what I may be doing wrong. Also, note that there appears to be no reference to the statement periodic_molecules = yes in the GROMACS manual as I did a search in the manual for periodic_molecules and the search came back empty. One error was not mentioning your GROMACS version. :-) Your grompp command line above is for some 3.x version, not some 4.x version. periodic_molecules is a 4.x feature (but mentioned only in section 7.3 IIRC). I've no idea how to solve your problem for 3.x, but if you can reasonably upgrade, you should. In the 3.x series, the option to use is pbc = full, but as Mark suggests, upgrading to 4.0.5 is probably a better idea. -Justin Mark Thanks. Darrell Date: Tue, 22 Sep 2009 15:07:03 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4ab85b77.10...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Hi Mark, I did not have the statement periodic_molecules = yes in the .mdp files. I only had the statement pbc=xyz in the .mdp files. So, I added the periodic_molecules = yes statement to the .mdp files and ran the simulation again. However, this did not appear to resolve the problem as I received the same warning. Well that's a pretty basic requirement that you needed to satisfy. Obviously you also need to re-generate your .tpr from the new .mdp. That'd be the most likely reason for an *identical* output. Have you done enough background reading (e.g. wiki page on Carbon Nanotube simulations) and/or gotten some experience with normal GROMACS simulations? Mark Date: Mon, 21 Sep 2009 16:56:48 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4ab723b0.6040...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Dear GROMACS-ians, I have created an infinite graphene sheet and upon running grompp, I get the following response: /Warning: 1-4 interaction between 10085 and 10445 at distance 19.679 which is larger than the 1-4 table size 1.000 nm Warning: 1-4 interaction between 9244 and 9963 at distance 19.553 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 These are ignored for the rest of the simulation/ I assume that atoms from opposite ends of the simulation box are being seen by GROMACS as being 1-4 neighbors as a result of the PBC, but the shortest distance between the atoms is not being observed. Is this the problem? Is this problem resulting in the system exploding? And, how do I resolve this problem? Did you use periodic_molecules = yes in your .mdp file? 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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] 1-4 interaction between atoms in PBC mode
Hi Justin, I am using version 3.3.3 and read through the version 3.3 manual but do not see an option to set pbc = full in this manual. I only see options to set pbc to xyz or no. Will setting pbc=full be recognized in GROAMCS version 3.3.3 and will this solve my problem? Thanks. Darrell Date: Tue, 22 Sep 2009 06:45:13 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4ab8aab9.7010...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Mark Abraham wrote: Darrell Koskinen wrote: Hi Mark, Yes, I have had success running many GROMACS simulations with a simple graphene sheet inside a box. I believe I have regenerated the .tpr file from the new .mdp as the very first command I issue is: grompp -np $NUM_PROCS -f em.mdp -c $GRO_FILE -p $TOP_FILE -o emtopol.tpr -n index.ndx Please advise me on what I may be doing wrong. Also, note that there appears to be no reference to the statement periodic_molecules = yes in the GROMACS manual as I did a search in the manual for periodic_molecules and the search came back empty. One error was not mentioning your GROMACS version. :-) Your grompp command line above is for some 3.x version, not some 4.x version. periodic_molecules is a 4.x feature (but mentioned only in section 7.3 IIRC). I've no idea how to solve your problem for 3.x, but if you can reasonably upgrade, you should. In the 3.x series, the option to use is pbc = full, but as Mark suggests, upgrading to 4.0.5 is probably a better idea. -Justin Mark Thanks. Darrell Date: Tue, 22 Sep 2009 15:07:03 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4ab85b77.10...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Hi Mark, I did not have the statement periodic_molecules = yes in the .mdp files. I only had the statement pbc=xyz in the .mdp files. So, I added the periodic_molecules = yes statement to the .mdp files and ran the simulation again. However, this did not appear to resolve the problem as I received the same warning. Well that's a pretty basic requirement that you needed to satisfy. Obviously you also need to re-generate your .tpr from the new .mdp. That'd be the most likely reason for an *identical* output. Have you done enough background reading (e.g. wiki page on Carbon Nanotube simulations) and/or gotten some experience with normal GROMACS simulations? Mark Date: Mon, 21 Sep 2009 16:56:48 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4ab723b0.6040...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Dear GROMACS-ians, I have created an infinite graphene sheet and upon running grompp, I get the following response: /Warning: 1-4 interaction between 10085 and 10445 at distance 19.679 which is larger than the 1-4 table size 1.000 nm Warning: 1-4 interaction between 9244 and 9963 at distance 19.553 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 These are ignored for the rest of the simulation/ I assume that atoms from opposite ends of the simulation box are being seen by GROMACS as being 1-4 neighbors as a result of the PBC, but the shortest distance between the atoms is not being observed. Is this the problem? Is this problem resulting in the system exploding? And, how do I resolve this problem? Did you use periodic_molecules = yes in your .mdp file? 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech
Re: [gmx-users] 1-4 interaction between atoms in PBC mode
darre...@ece.ubc.ca wrote: Hi Justin, I am using version 3.3.3 and read through the version 3.3 manual but do not see an option to set pbc = full in this manual. I only see options to set pbc to xyz or no. Will setting pbc=full be recognized in GROAMCS version 3.3.3 and will this solve my problem? Yes, it will. I don't know why it was never in the documetation. -Justin Thanks. Darrell Date: Tue, 22 Sep 2009 06:45:13 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4ab8aab9.7010...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Mark Abraham wrote: Darrell Koskinen wrote: Hi Mark, Yes, I have had success running many GROMACS simulations with a simple graphene sheet inside a box. I believe I have regenerated the .tpr file from the new .mdp as the very first command I issue is: grompp -np $NUM_PROCS -f em.mdp -c $GRO_FILE -p $TOP_FILE -o emtopol.tpr -n index.ndx Please advise me on what I may be doing wrong. Also, note that there appears to be no reference to the statement periodic_molecules = yes in the GROMACS manual as I did a search in the manual for periodic_molecules and the search came back empty. One error was not mentioning your GROMACS version. :-) Your grompp command line above is for some 3.x version, not some 4.x version. periodic_molecules is a 4.x feature (but mentioned only in section 7.3 IIRC). I've no idea how to solve your problem for 3.x, but if you can reasonably upgrade, you should. In the 3.x series, the option to use is pbc = full, but as Mark suggests, upgrading to 4.0.5 is probably a better idea. -Justin Mark Thanks. Darrell Date: Tue, 22 Sep 2009 15:07:03 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4ab85b77.10...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Hi Mark, I did not have the statement periodic_molecules = yes in the .mdp files. I only had the statement pbc=xyz in the .mdp files. So, I added the periodic_molecules = yes statement to the .mdp files and ran the simulation again. However, this did not appear to resolve the problem as I received the same warning. Well that's a pretty basic requirement that you needed to satisfy. Obviously you also need to re-generate your .tpr from the new .mdp. That'd be the most likely reason for an *identical* output. Have you done enough background reading (e.g. wiki page on Carbon Nanotube simulations) and/or gotten some experience with normal GROMACS simulations? Mark Date: Mon, 21 Sep 2009 16:56:48 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4ab723b0.6040...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Dear GROMACS-ians, I have created an infinite graphene sheet and upon running grompp, I get the following response: /Warning: 1-4 interaction between 10085 and 10445 at distance 19.679 which is larger than the 1-4 table size 1.000 nm Warning: 1-4 interaction between 9244 and 9963 at distance 19.553 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 These are ignored for the rest of the simulation/ I assume that atoms from opposite ends of the simulation box are being seen by GROMACS as being 1-4 neighbors as a result of the PBC, but the shortest distance between the atoms is not being observed. Is this the problem? Is this problem resulting in the system exploding? And, how do I resolve this problem? Did you use periodic_molecules = yes in your .mdp file? 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry
Re: [gmx-users] 1-4 interaction between atoms in PBC mode
Justin A. Lemkul wrote: darre...@ece.ubc.ca wrote: Hi Justin, I am using version 3.3.3 and read through the version 3.3 manual but do not see an option to set pbc = full in this manual. I only see options to set pbc to xyz or no. Will setting pbc=full be recognized in GROAMCS version 3.3.3 and will this solve my problem? Yes, it will. I don't know why it was never in the documetation. I should amend that. Yes, the option will be recognized. It is probably in line with what you need for an infinite molecule. No guarantees that anything will work just because I say it will, although that would be so very convenient... :) -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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] 1-4 interaction between atoms in PBC mode
Dear GROMACS-ians, I have created an infinite graphene sheet and upon running grompp, I get the following response: /Warning: 1-4 interaction between 10085 and 10445 at distance 19.679 which is larger than the 1-4 table size 1.000 nm Warning: 1-4 interaction between 9244 and 9963 at distance 19.553 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 These are ignored for the rest of the simulation/ I assume that atoms from opposite ends of the simulation box are being seen by GROMACS as being 1-4 neighbors as a result of the PBC, but the shortest distance between the atoms is not being observed. Is this the problem? Is this problem resulting in the system exploding? And, how do I resolve this problem? Thanks. Darrell ___ 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] 1-4 interaction between atoms in PBC mode
Darrell Koskinen wrote: Dear GROMACS-ians, I have created an infinite graphene sheet and upon running grompp, I get the following response: /Warning: 1-4 interaction between 10085 and 10445 at distance 19.679 which is larger than the 1-4 table size 1.000 nm Warning: 1-4 interaction between 9244 and 9963 at distance 19.553 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 These are ignored for the rest of the simulation/ I assume that atoms from opposite ends of the simulation box are being seen by GROMACS as being 1-4 neighbors as a result of the PBC, but the shortest distance between the atoms is not being observed. Is this the problem? Is this problem resulting in the system exploding? And, how do I resolve this problem? Did you use periodic_molecules = yes in your .mdp file? 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] 1-4 interaction between atoms in PBC mode
I assume that atoms from opposite ends of the simulation box are being seen by GROMACS as being 1-4 neighbors as a result of the PBC, Are you sure? have you looked at the last good frame before this message? GMX treats PBC as it should during MD neighbour search, so maybe this is a pair that was initially close and interacting, but later moved away from each other. but the shortest distance between the atoms is not being observed. Is this the problem? Is this problem resulting in the system exploding? And, how do I resolve this problem? If you are sure that everything else is ok, then extend the table extension. Two other things to work around this are either reduce timestep or check that your definition of the box is as it should. --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
[gmx-users] 1-4 interaction between atoms in PBC mode
Hi Mark, I did not have the statement periodic_molecules = yes in the .mdp files. I only had the statement pbc=xyz in the .mdp files. So, I added the periodic_molecules = yes statement to the .mdp files and ran the simulation again. However, this did not appear to resolve the problem as I received the same warning. Please advise. Darrell Date: Mon, 21 Sep 2009 16:56:48 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4ab723b0.6040...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Dear GROMACS-ians, I have created an infinite graphene sheet and upon running grompp, I get the following response: /Warning: 1-4 interaction between 10085 and 10445 at distance 19.679 which is larger than the 1-4 table size 1.000 nm Warning: 1-4 interaction between 9244 and 9963 at distance 19.553 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 These are ignored for the rest of the simulation/ I assume that atoms from opposite ends of the simulation box are being seen by GROMACS as being 1-4 neighbors as a result of the PBC, but the shortest distance between the atoms is not being observed. Is this the problem? Is this problem resulting in the system exploding? And, how do I resolve this problem? Did you use periodic_molecules = yes in your .mdp file? 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] 1-4 interaction between atoms in PBC mode
Darrell Koskinen wrote: Hi Mark, I did not have the statement periodic_molecules = yes in the .mdp files. I only had the statement pbc=xyz in the .mdp files. So, I added the periodic_molecules = yes statement to the .mdp files and ran the simulation again. However, this did not appear to resolve the problem as I received the same warning. Well that's a pretty basic requirement that you needed to satisfy. Obviously you also need to re-generate your .tpr from the new .mdp. That'd be the most likely reason for an *identical* output. Have you done enough background reading (e.g. wiki page on Carbon Nanotube simulations) and/or gotten some experience with normal GROMACS simulations? Mark Date: Mon, 21 Sep 2009 16:56:48 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4ab723b0.6040...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Dear GROMACS-ians, I have created an infinite graphene sheet and upon running grompp, I get the following response: /Warning: 1-4 interaction between 10085 and 10445 at distance 19.679 which is larger than the 1-4 table size 1.000 nm Warning: 1-4 interaction between 9244 and 9963 at distance 19.553 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 These are ignored for the rest of the simulation/ I assume that atoms from opposite ends of the simulation box are being seen by GROMACS as being 1-4 neighbors as a result of the PBC, but the shortest distance between the atoms is not being observed. Is this the problem? Is this problem resulting in the system exploding? And, how do I resolve this problem? Did you use periodic_molecules = yes in your .mdp file? 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
