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-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: membrane simulations (Justin Lemkul) > 2. interaction energy using g_enemat (Poojari, Chetan) > 3. R: Re: [gmx-users] Rotation Constraints - PMF + rerun > (battis...@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 <jalem...@vt.edu> > Subject: Re: [gmx-users] membrane simulations > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <51efb6d5.2060...@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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > > > ------------------------------ > > Message: 2 > Date: Wed, 24 Jul 2013 11:47:59 +0000 > From: "Poojari, Chetan" <c.pooj...@fz-juelich.de> > Subject: [gmx-users] interaction energy using g_enemat > To: "gmx-users@gromacs.org" <gmx-users@gromacs.org> > Message-ID: > < > 603fda448cf1c3419be07631a63a3ccf1350c...@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 > > > > ------------------------------------------------------------------------------------------------ > > ------------------------------------------------------------------------------------------------ > Forschungszentrum Juelich GmbH > 52425 Juelich > Sitz der Gesellschaft: Juelich > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher > Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), > Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, > Prof. Dr. Sebastian M. Schmidt > > ------------------------------------------------------------------------------------------------ > > ------------------------------------------------------------------------------------------------ > > Das Forschungszentrum oeffnet seine Tueren am Sonntag, 29. September, von > 10:00 bis 17:00 Uhr: http://www.tagderneugier.de > > > ------------------------------ > > Message: 3 > Date: Wed, 24 Jul 2013 13:59:18 +0200 (CEST) > From: "battis...@libero.it" <battis...@libero.it> > Subject: R: Re: [gmx-users] Rotation Constraints - PMF + rerun > To: gmx-users@gromacs.org > Message-ID: <1443239804.28991361374667158368.JavaMail.actor@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: ckut...@gwdg.de > >Data: 24/07/2013 13.09 > >A: "battis...@libero.it"<battis...@libero.it>, "Discussion list for > GROMACS > users"<gmx-users@gromacs.org> > >Ogg: Re: [gmx-users] Rotation Constraints - PMF + rerun > > > >On Jul 24, 2013, at 12:30 PM, battis...@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: ckut...@gwdg.de > >>> Data: 23/07/2013 13.09 > >>> A: "battis...@libero.it"<battis...@libero.it>, "Discussion list for > GROMACS > >> users"<gmx-users@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, battis...@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@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-requ...@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@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-requ...@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.wa...@chemie.tu-freiberg.de> > Subject: Re: [gmx-users] OpenSuse 12.1 + CUDA Installation Error > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <51efc9a6.4050...@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 <nganoucoll...@gmail.com> > Subject: [gmx-users] Index error > To: gmx-users@gromacs.org > Message-ID: > < > camcnyho4djerpevd569vjbw3phhed+ej7a8rqwy8zqvcqgm...@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 <jalem...@vt.edu> > Subject: Re: [gmx-users] Index error > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <51efca5d.4030...@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 > > 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 112 > ******************************************* > -- 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. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
