[gmx-users] Re: gmx-users Digest, Vol 111, Issue 112
Collins Nganou
nganoucollins at gmail.com
Thu Jul 25 19:47:15 CEST 2013
Dear Justin,
Thanks for your answer...
I move so far...
My aim was to ask gromacs to read directly a modify protein SOL+NA, not
protein SOL NA
But I have not succeed so far.
Best regards
Collins
On Wed, Jul 24, 2013 at 8:38 AM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Re: membrane simulations (Justin Lemkul)
> 2. interaction energy using g_enemat (Poojari, Chetan)
> 3. R: Re: [gmx-users] Rotation Constraints - PMF + rerun
> (battistia at libero.it)
> 4. Re: OpenSuse 12.1 + CUDA Installation Error (Mirco Wahab)
> 5. Index error (Collins Nganou)
> 6. Re: Index error (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 24 Jul 2013 07:13:25 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] membrane simulations
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <51EFB6D5.2060406 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 7/24/13 2:55 AM, Sathish Kumar wrote:
> > I am doing simulation of metal clusters with membranes by position
> restrain
> > (with f=1000) the membrane. In this simulation the structure of metal
> > cluster is collapsed after entering into membrane. I want to preserves
> its
> > structure with out doing position restrain the metal cluster because it
> has
> > to move. Can you please suggest me how can I solve this problem.
> >
>
> Geometry is a function of the topology. Setting correct parameters for
> whatever
> the desired or expected geometry is should alleviate the issue.
>
> -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: Wed, 24 Jul 2013 11:47:59 +0000
> From: "Poojari, Chetan" <c.poojari at fz-juelich.de>
> Subject: [gmx-users] interaction energy using g_enemat
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Message-ID:
> <
> 603FDA448CF1C3419BE07631A63A3CCF1350C905 at MBX2010-K01.ad.fz-juelich.de>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear All,
>
> I want to calculate interaction energy per residue.
>
> Below is the command i used:
>
> g_enemat -f strand.edr -groups groups.dat -emat strand_emat.xpm
>
>
> my groups.dat file contains these lines:
>
> 3
> strand1_SER_34
> strand1_THR_36
> strand1_TYR_37
>
>
> When i execute the above g_enemat command i get the below error message:
>
> WARNING! could not find group LJ-SR:strand1_SER_34 -strand1_THR_36
> (34,36)in energy file
> WARNING! could not find group Coul-SR:strand1_SER_34 -strand1_TYR_37
> (34,37)in energy file
>
>
> My strand.edr file looks like this:
>
> LJ-SR:strand1_SER_34-strand1_THR_36
> Coul-SR:strand1_SER_34-strand1_TYR_37
>
>
>
> Please can I get some suggestions on how to get around this problem.
>
>
> Kind Regards,
> Chetan
>
>
>
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>
> ------------------------------
>
> Message: 3
> Date: Wed, 24 Jul 2013 13:59:18 +0200 (CEST)
> From: "battistia at libero.it" <battistia at libero.it>
> Subject: R: Re: [gmx-users] Rotation Constraints - PMF + rerun
> To: gmx-users at gromacs.org
> Message-ID: <1443239804.28991361374667158368.JavaMail.actor at webmail7>
> Content-Type: text/plain;charset="UTF-8"
>
> in my traj.xtc file there are 1 frame every 10 ps from 0 ps to 10000 ps,
> therefore in total 1001 frames.
>
> I tried -x trj.xtc instead -o trj.trr, but mdrun has generated a file
> trj.xtc.
> trr
>
> Many thanks!
>
> Anna
>
>
> >----Messaggio originale----
> >Da: ckutzne at gwdg.de
> >Data: 24/07/2013 13.09
> >A: "battistia at libero.it"<battistia at libero.it>, "Discussion list for
> GROMACS
> users"<gmx-users at gromacs.org>
> >Ogg: Re: [gmx-users] Rotation Constraints - PMF + rerun
> >
> >On Jul 24, 2013, at 12:30 PM, battistia at libero.it wrote:
> >
> >> Dear Carsten,
> >>
> >> Thank you very much for your very useful help!
> >> I'm making some tries to test the orire options that probably will solve
> my
> >> problem.
> >>
> >> In order to do not waste resource, I thought using the rerun option of
> mdrun I
> >> can use the trajectories generated before, where my mistake was to allow
> the
> >> rotation of my structure.
> >> So I generated a new topol.tpr file changing the orire options in the
> mdp
> and
> >> I made:
> >>
> >> 1. mdrun -rerun ../traj.xtc -s topol.tpr -o trj.trr
> >> 2. trjcat -f traj.trr -o trajout.xtc
> >>
> >> but in the trajout.xtc there is only one point as I can check for
> example
> >Hm, I am not sure, maybe you need to use -x trj.xtc instead of -o trj.trr
> >to trigger output of all .xtc frames. How many frames are in ../traj.xtc?
> >
> >Carsten
> >
> >> with:
> >> 3. g_gyrate -f trajout.xtc -s topol.tpr -n index.ndx
> >>
> >>
> >> Could you confirm me that it is not possible follow this idea?
> >> In fact I suppose that this method it is not applicable; but it is
> necessary
> >> to generate a new trajectory, because the angular restraints modify
> completely
> >> the trajectory.
> >>
> >> Or, just to be sure, did I not made the things in the right way?
> >>
> >> Thank you very much!
> >>
> >> Anna
> >>
> >>
> >>> ----Messaggio originale----
> >>> Da: ckutzne at gwdg.de
> >>> Data: 23/07/2013 13.09
> >>> A: "battistia at libero.it"<battistia at libero.it>, "Discussion list for
> GROMACS
> >> users"<gmx-users at gromacs.org>
> >>> Ogg: Re: [gmx-users] Rotation Constraints - PMF
> >>>
> >>> Hi Anna,
> >>>
> >>> please have a look at the Enforced Rotation Section in the Gromacs 4.6
> >> manual.
> >>> You can restrain the angle of rotation about an axis by setting the
> rotation
> >> rate
> >>> to zero. There is also a 4.5 add-on available with rotational
> restraints
> in
> >>> the Gromacs git repository (branch "rotation"). For more info you may
> want
> to
> >>> look at this page:
> >>>
> >>> http://www.mpibpc.mpg.de/grubmueller/rotation
> >>>
> >>> Best,
> >>> Carsten
> >>>
> >>>
> >>> On Jul 23, 2013, at 12:18 PM, battistia at libero.it wrote:
> >>>
> >>>> Dear user and expert,
> >>>> I'd like ask you a suggestion about a problem that I will try present
> you
> >> schematically.
> >>>> I have got a structure "s" and I have generated the topolgy file itp
> for
> it.
> >> A number of separate "s" in turn generate a complex structure A, that is
> >> characterized by a cylindrical shape.
> >>>> Now, I constructed a system with two cylindrical structures, A and B
> (in
> >> total made by 64 "s" structures), and I'd like make an Umbrella Sampling
> >> calculation in order to study the PMF varying the distance between A
> and B.
> >>>>
> >>>> My problem is that I'd like fix the orientation of the axis of each
> >> structure A and B long the z axis, during the dynamics.
> >>>> So I need to put a force into the system or a constrain, such that
> when
> the
> >> axis of A or B rotates respect to z axis, the force puts back the axis
> of
> the
> >> structure in the z direction.
> >>>>
> >>>> It this possible? If it is so, could you tell me how to do that?
> >>>> Than you very much,
> >>>> Anna
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> gmx-users mailing list gmx-users at 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-request at gromacs.org.
> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >>>
> >>> --
> >>> Dr. Carsten Kutzner
> >>> Max Planck Institute for Biophysical Chemistry
> >>> Theoretical and Computational Biophysics
> >>> Am Fassberg 11, 37077 Goettingen, Germany
> >>> Tel. +49-551-2012313, Fax: +49-551-2012302
> >>> http://www.mpibpc.mpg.de/grubmueller/kutzner
> >>> http://www.mpibpc.mpg.de/grubmueller/sppexa
> >>>
> >>>
> >>
> >>
> >> --
> >> gmx-users mailing list gmx-users at 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-request at gromacs.org.
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >
> >--
> >Dr. Carsten Kutzner
> >Max Planck Institute for Biophysical Chemistry
> >Theoretical and Computational Biophysics
> >Am Fassberg 11, 37077 Goettingen, Germany
> >Tel. +49-551-2012313, Fax: +49-551-2012302
> >http://www.mpibpc.mpg.de/grubmueller/kutzner
> >http://www.mpibpc.mpg.de/grubmueller/sppexa
> >
> >
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 24 Jul 2013 14:33:42 +0200
> From: Mirco Wahab <mirco.wahab at chemie.tu-freiberg.de>
> Subject: Re: [gmx-users] OpenSuse 12.1 + CUDA Installation Error
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <51EFC9A6.4050503 at chemie.tu-freiberg.de>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> On 24.07.2013 04:08, Carlos Bueno wrote:
> > *Hi,*
> > *I keep getting errors when I try to install gromacs in OpenSuse 12.1.*
> > *I have installed cuda 5.0 and the nvidia cards. **I have tried with
> > different parameters for cmake:*
>
> How did you install Cuda5? What did you install and how?
>
> I have one OpenSuSE 12.1 box that works as a cluster head
> and serves to gpu-clusters. Every software except the
> nvidia gpu driver is installed on this box for usage by
> the nodes.
>
> Installing a gpu-ready OpenSuSE 12.1 involves (for example, YMMD)
> * add community- and extra-repositories through yast/repositories,
> these involve (here):
> (a) included in yast/repositories (activate only)
> Packman Repository
> openSUSE BuildService - devel:languages:perl
> openSUSE BuildService - devel:languages:python
> Education
> science
> (b) extra (add manually or ba script)
> devel:/tools
> devel:/libraries:/c_c++
> devel:/gcc
> you can do the latter by script:
> #
> #!/bin/sh
>
> Uri[1]="
> http://download.opensuse.org/repositories/devel:/tools/openSUSE_12.1/"
> Name[1]="devel:/tools"
>
> Uri[2]="
> http://download.opensuse.org/repositories/devel:/libraries:/c_c++/openSUSE_12.1/
> "
> Name[2]="devel:/libraries:/c_c++"
>
> Uri[3]="
> http://download.opensuse.org/repositories/devel:/gcc/openSUSE_12.1/"
> Name[3]="devel:/gcc"
> #
> for i in 1 2 3; do
> zypper --gpg-auto-import-keys ar ${Uri[i]} ${Name[i]}
> zypper modifyrepo --refresh ${Name[i]}
> done
> #
>
> * install gcc 4.6 / g++ 4.6 through yast
> * install fftw 3.3.3 through yast, look for the following packages:
> gpuclu:~ # rpm -qa |grep fftw
> libfftw3-3-3.3.3-5.1.x86_64
> fftw3-devel-3.3.3-5.1.x86_64
> fftw3-3.3-18.1.3.x86_64
> fftw3-threads-3.3-18.1.3.x86_64
> fftw3-threads-devel-3.3.3-5.1.x86_64
> libfftw3_threads3-3.3.3-5.1.x86_64
> * install blas-devel, lapack-devel, gsl-devel through yast
> * Important: remove everything Nvidia-related stuff through yast, reboot
> * download and install (compile) the gpu driver
> NVIDIA-Linux-x86_64-319.32.run
> check if it functions properly (after reboot)
> * download and install CUDA from Nvidia:
> cuda_5.0.35_linux_64_suse12.1-1.run
>
> if everything works, the command
> nvidia-smi
> should display some meaningful output.
>
>
>
> my € 0.05
>
> M.
>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 24 Jul 2013 08:34:18 -0400
> From: Collins Nganou <nganoucollins at gmail.com>
> Subject: [gmx-users] Index error
> To: gmx-users at gromacs.org
> Message-ID:
> <
> CAMCNYHO4DJeRPEvd569vjbW3PHheD+eJ7A8RqWy8ZQVCqgmcyg at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Users,
>
> I would like to know if anyone may help me understand how to update the
> index file.
> I am trying to simulate a dna in solution.
> I have relaxed a Solvent with attached min.mdp file without problem. in
> the second step I was intended to relax SOL + Na DNA with 20ps.mdp. But
> the index file did not work.
> I have trying to generate an index file using the file.gro from min.mdp but
> it doesn't work.
>
> Below is the obtained error.
>
> Generated 2211 of the 2211 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 2211 of the 2211 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'DNA_chain_B'
> turning H bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning H bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'NA'
> turning H bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'CL'
> turning H bonds into constraints...
> Velocities were taken from a Maxwell distribution at 10 K
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/kernel/readir.c, line:
> 1332
>
> Fatal error:
> Group NA+SOL referenced in the .mdp file was not found in the index file.
> Group names must match either [moleculetype] names or custom index group
> names, in which case you must supply an index file to the '-n' option
> of grompp.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
>
> I am looking forward to have any suggestion that might help me in this
> case.
>
> I wish all of you a wonderful day.
>
> Collins
>
> ------------------------------
>
> Message: 6
> Date: Wed, 24 Jul 2013 08:36:45 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Index error
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <51EFCA5D.4030105 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 7/24/13 8:34 AM, Collins Nganou wrote:
> > Dear Users,
> >
> > I would like to know if anyone may help me understand how to update the
> > index file.
> > I am trying to simulate a dna in solution.
> > I have relaxed a Solvent with attached min.mdp file without problem. in
> > the second step I was intended to relax SOL + Na DNA with 20ps.mdp. But
> > the index file did not work.
> > I have trying to generate an index file using the file.gro from min.mdp
> but
> > it doesn't work.
> >
>
> It is simple to merge solvent and ion groups. See tutorial material or
> type
> 'help' at the make_ndx prompt. We can't help you if we don't know what
> you did.
>
> > Below is the obtained error.
> >
> > Generated 2211 of the 2211 non-bonded parameter combinations
> > Generating 1-4 interactions: fudge = 0.5
> > Generated 2211 of the 2211 1-4 parameter combinations
> > Excluding 3 bonded neighbours molecule type 'DNA_chain_B'
> > turning H bonds into constraints...
> > Excluding 2 bonded neighbours molecule type 'SOL'
> > turning H bonds into constraints...
> > Excluding 1 bonded neighbours molecule type 'NA'
> > turning H bonds into constraints...
> > Excluding 1 bonded neighbours molecule type 'CL'
> > turning H bonds into constraints...
> > Velocities were taken from a Maxwell distribution at 10 K
> >
> > -------------------------------------------------------
> > Program grompp, VERSION 4.5.5
> > Source code file: /build/buildd/gromacs-4.5.5/src/kernel/readir.c, line:
> > 1332
> >
> > Fatal error:
> > Group NA+SOL referenced in the .mdp file was not found in the index file.
> > Group names must match either [moleculetype] names or custom index group
> > names, in which case you must supply an index file to the '-n' option
> > of grompp.
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> >
>
> If you use make_ndx, group names will never contain + signs. Merged
> groups are
> joined via _ (underscore), but it sounds like you haven't even gotten that
> far,
> given the statement above.
>
> -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
>
> ==================================================
>
>
> ------------------------------
>
> --
> gmx-users mailing list
> gmx-users at 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 112
> *******************************************
>
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