Dear Justin, Thank you....
for your suggestion... Best regards Collins On Mon, Jul 22, 2013 at 10:00 AM, <gmx-users-requ...@gromacs.org> wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: mdrun error (Justin Lemkul) > 2. LAMBADA and InflateGRO2 (Atila Petrosian) > 3. Persistence length calculation using g_polystat > (Mohan maruthi sena) > 4. Initial cell size is smaller than the cell size limit.. > (Kavyashree M) > 5. Re: Initial cell size is smaller than the cell size limit.. > (Justin Lemkul) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 21 Jul 2013 07:14:30 -0400 > From: Justin Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] mdrun error > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <51ebc296.1080...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 7/21/13 12:18 AM, Collins Nganou wrote: > > Dear Users, > > > > when trying to run the following command: > > mdrun -v -deffnm protein-EM-solvated -c protein-EM-solvated.pdb > > I have received the error below. > > > > > > > > Reading file dna-EM-solvated.tpr, VERSION 4.5.5 (single precision) > > Starting 2 threads > > > > ------------------------------------------------------- > > Program mdrun, VERSION 4.5.5 > > Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/domdec.c, line: > 6005 > > > > Fatal error: > > Domain decomposition does not support simple neighbor searching, use grid > > searching or use particle decomposition > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > > > > > I am looking any suggestion that can help me to overcome this error. > > > > Not all combinations of options are compatible, and mdrun already told you > exactly what to do. If you want to use DD, you can't use "nstype = > simple," so > you have to invoke mdrun -pd in this case or otherwise switch to "nstype = > grid." How you proceed depends on what you're trying to achieve with your > .mdp > settings. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > > > ------------------------------ > > Message: 2 > Date: Sun, 21 Jul 2013 16:43:16 +0430 > From: Atila Petrosian <atila.petros...@gmail.com> > Subject: [gmx-users] LAMBADA and InflateGRO2 > To: gmx-users <gmx-users@gromacs.org> > Message-ID: > < > caon_0oxo2_zs9h5tifjsa6e7lt7r+8ajqroyfsdvhmp90r2...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear gromacs users > > I want to use LAMBADA and InflateGRO2 to create a system containing > dopc lipid + cholesterol + drug. > > When I use > ~/lib/lambada/lambada_rc1/lambada -f1 drug.gro -f2 lipid_chol.gro > > I encountered with > > Illegal division by zero at /home/karami/lib/lambada/ > lambada_rc1/lambada line 677. > > > How to resolve this issue? Please help me to do this step. > > Best wishes > > > ------------------------------ > > Message: 3 > Date: Sun, 21 Jul 2013 23:27:26 +0530 > From: Mohan maruthi sena <maruthi.s...@gmail.com> > Subject: [gmx-users] Persistence length calculation using g_polystat > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <CAGbPF0V5mT5N4ZK4LVguaVZZ36PU= > iuwpbdlumdgzwxfsub...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear gmx users, > I would like to calculate persistence length of > DNA using gromacs command g_polystat . The out put file of persists.xvg > contains persistence length in number of bonds and it shows that the > average persistence length = 4.3 bonds. How can we convert no of bonds in > to length(nm)?. Please suggest me a way to solve this. > > > Thanks for a reply in advance, > > > With regards, > Mohan > > > ------------------------------ > > Message: 4 > Date: Mon, 22 Jul 2013 10:50:00 +0530 > From: Kavyashree M <hmkv...@gmail.com> > Subject: [gmx-users] Initial cell size is smaller than the cell size > limit.. > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > < > caplgqjqw5f5yedmkw64ezgqmbms2fytykpx8njjst9wjfeo...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear users, > > While running a ligand bound MD using AMber03 force field. I got the > following error > after ~ 4.9 ns > The initial cell size (1.247705) is smaller than the cell size limit > (1.586683), change options -dd, -rdd or -rcon, see the log file for details > > Initially I ran using 64 nodes (till 3.3ns). later on I shifted the > trajectory to another > machine and ran using 8 cores. It ran fine till 4.926ns. Suddenly it > stopped with the above error. > > Kindly provide some guidance. > > Thank you > Regards > Kavya > > > ------------------------------ > > Message: 5 > Date: Mon, 22 Jul 2013 05:32:42 -0400 > From: Justin Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] Initial cell size is smaller than the cell > size limit.. > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <51ecfc3a.1060...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 7/22/13 1:20 AM, Kavyashree M wrote: > > Dear users, > > > > While running a ligand bound MD using AMber03 force field. I got the > > following error > > after ~ 4.9 ns > > The initial cell size (1.247705) is smaller than the cell size limit > > (1.586683), change options -dd, -rdd or -rcon, see the log file for > details > > > > Initially I ran using 64 nodes (till 3.3ns). later on I shifted the > > trajectory to another > > machine and ran using 8 cores. It ran fine till 4.926ns. Suddenly it > > stopped with the above error. > > > > Kindly provide some guidance. > > > > You can't necessarily parallelize a system across any arbitrary number of > cores. > The DD algorithm sets certain size limitations on the cells, which you > are > violating during the simulation. A slight reduction in the number of cores > should solve the issue (though you can't restart from a checkpoint and may > have > to start the run over). > > For a more detailed explanation of the error message, check the archive - > the > algorithm, the settings, and factors governing cell size have all been > discussed > before in reference to the same error. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > > > ------------------------------ > > -- > 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/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 111, Issue 101 > ******************************************* > -- 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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