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 list 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. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> _______________________________________________ >> gmx-users mailing list 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. >> 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 list 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. Can't post? Read http://www.gromacs.org/mailing_lists/users.php