[gmx-users] Re: gmx-users Digest, Vol 111, Issue 101
Collins Nganou
nganoucollins at gmail.com
Tue Jul 23 19:55:34 CEST 2013
Dear Justin,
Thank you....
for your suggestion...
Best regards
Collins
On Mon, Jul 22, 2013 at 10:00 AM, <gmx-users-request at gromacs.org> wrote:
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> 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 <jalemkul at vt.edu>
> Subject: Re: [gmx-users] mdrun error
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <51EBC296.1080704 at 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
> ==================================================
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 21 Jul 2013 16:43:16 +0430
> From: Atila Petrosian <atila.petrosian at gmail.com>
> Subject: [gmx-users] LAMBADA and InflateGRO2
> To: gmx-users <gmx-users at gromacs.org>
> Message-ID:
> <
> CAON_0oXO2_Zs9H5tiFjsa6E7Lt7R+8aJQROYfSDvhMp90R2qPA at 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.sena at gmail.com>
> Subject: [gmx-users] Persistence length calculation using g_polystat
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CAGbPF0V5mT5N4ZK4LVguaVZZ36PU=
> iUWpBdLuMdGzwxfsubJMg at 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 <hmkvsri at gmail.com>
> Subject: [gmx-users] Initial cell size is smaller than the cell size
> limit..
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <
> CAPLGqjqw5f5yEdMKW64EzGqmBms2fYTYKpx8nJJST9wJfeoE_Q at 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 <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Initial cell size is smaller than the cell
> size limit..
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <51ECFC3A.1060700 at 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
> ==================================================
>
>
> ------------------------------
>
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> End of gmx-users Digest, Vol 111, Issue 101
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