Re: [gmx-users] mpi- gromacs
g_energy needs input to supply which energy item you would like to output. To automate this, use echo -e "1\n2\n" | g_energy_mpi -f minim_ener.edr -o minim_ener.xvg However, I don't see any point to run g_energy with mpi. If you have (mis-)compiled it with MPI, build a non-MPI version for all analysis programs. Regards, Yang Ye On 10/30/08 11:40 AM, Chih-Ying Lin wrote: Hi Here is my pdb file. #!/bin/bash #PBS -l nodes=2 cat $PBS_NODEFILE echo Working directory is $PBS_O_WORKDIR cd $PBS_O_WORKDIR mpirun -np 2 g_energy_mpi -f minim_ener.edr -o minim_ener.xvg 11 0 Then, it showed Fatal error: No energy terms selected How to fix the problem Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Fatal error, spc.itp", line 41
Chih-Ying Lin wrote: Hi I still have no idea about this. Some useful information from Archive is the application on using GROMACS' spc topology with ffamber. But, I am using Gromacs straight without ffamber. How should I solve the problem? We don't necessarily remember the context of your problem - since it's not immediately important to us and nobody's paying us to do so. You need either to reply to an old email that does have some of the discussion, or describe it again. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mpi- gromacs
Chih-Ying Lin wrote: Hi Here is my pdb file. #!/bin/bash #PBS -l nodes=2 cat $PBS_NODEFILE echo Working directory is $PBS_O_WORKDIR cd $PBS_O_WORKDIR mpirun -np 2 g_energy_mpi -f minim_ener.edr -o minim_ener.xvg 11 0 Then, it showed Fatal error: No energy terms selected g_energy is not MPI-aware - see http://wiki.gromacs.org/index.php/Installation#Using_MPI - so don't compile it, and don't attempt to run it in parallel. Most of the GROMACS utility programs are intended to run from the command line rather than on a compute cluster. The above syntax is not how to use g_energy in an automated fashion. See http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive for discussion of your options. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mpi- gromacs
Hi Here is my pdb file. #!/bin/bash #PBS -l nodes=2 cat $PBS_NODEFILE echo Working directory is $PBS_O_WORKDIR cd $PBS_O_WORKDIR mpirun -np 2 g_energy_mpi -f minim_ener.edr -o minim_ener.xvg 11 0 Then, it showed Fatal error: No energy terms selected How to fix the problem Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fatal error, spc.itp", line 41
Hi I still have no idea about this. Some useful information from Archive is the application on using GROMACS' spc topology with ffamber. But, I am using Gromacs straight without ffamber. How should I solve the problem? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] 4fs timestep in gromacs 4.0
Hello, I am interested in trying the 4 fs timestep options for an opls-protein/tip4p-water system. I will of course do some quick NVE tests to ensure that the energy does not drift massively, and also do some other tests that look at some properties that should equilibrate rather quickly. Also, I realize that there is no substitute for reading the literature. Still, I am hoping to get some indication of how this was intended to be utilized in gmx4. Can I just run pdb2gmx -vsite -heavyh and apply LINCS to all-bonds? The information in the gmx4 manual is nicely detailed about how each type of hydrogen should be treated, but I am not clear how to achieve this in my .top. Searches for vsite and heavyh reading only the 2008 posts did not give me much indication about this. Thanks, Chris. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] oplsaa in Gromacs 4.0
friendli wrote: Dear all, Are the topology components of OPLSAA force field explicitly displayed in Gromacs 4.0? I mean the bond, angle, dihedral types(or parameters) following the composed atoms. They are not showed in .top file when oplsaa FF is used, not like other force field, e.g. Gromos96. The different force fields are constructed differently. If you look in the .itp files #included in your .top file, you will see the functional forms that are "looked up" by the atom types and numbers that are in the .top file. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] oplsaa in Gromacs 4.0
Dear all, Are the topology components of OPLSAA force field explicitly displayed in Gromacs 4.0? I mean the bond, angle, dihedral types(or parameters) following the composed atoms. They are not showed in .top file when oplsaa FF is used, not like other force field, e.g. Gromos96. thanks Qiang ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_rdf: "not in list" error
Hi, When attempting to use g_rdf to calculate the structure factor for a simple Argon liquid, I get the following error: --- Program g_rdf_d, VERSION 3.3.3 Source code file: gmx_rdf.c, line: 622 Fatal error: Error: atom (Ar) not in list (5 types checked)! --- I have looked through the archives and seen other users ask similar questions, but I was unable to find an answer in a reply. Is this a problem that can be solved by changing the input files that I supply to g_rdf, or will fixing this involve editing the source code for this analysis tool? Thanks in advance, John ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs 4.0 installation problem
Chavatte Philippe wrote: Hi, We are trying to install gromacs 4.0 on our new SGI cluster running under RHEL5. The configure script run fine (./configure –prefix =/install-dir). But an error occurs during the building (make) : cc -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\"/data1/soft/linux/gromacs-4.0/share/top\" -I/data1/soft/linux/fftw-3.1.3/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT grompp.o -MD -MP -MF .deps/grompp.Tpo -c -o grompp.o grompp.c mv -f .deps/grompp.Tpo .deps/grompp.Po /bin/sh ../../libtool --tag=CC --mode=link cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -L/data1/soft/linux/fftw-3.1.3/lib -o grompp grompp.o libgmxpreprocess.la ../mdlib/libmd.la ../gmxlib/libgmx.la -L/usr/lib64 -lnsl -lfftw3f -lm -lX11 cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -o grompp grompp.o -L/data1/soft/linux/fftw-3.1.3/lib ./.libs/libgmxpreprocess.a -L/usr/lib64 ../mdlib/.libs/libmd.a ../gmxlib/.libs/libgmx.a -lnsl /data1/soft/linux/fftw-3.1.3/lib/libfftw3f.a -lm -lX11 /usr/bin/ld: cannot find -lX11 That's indicative of something weird going on. configure should have looked for this library and found it. Nonetheless, it's only used in one utility in GROMACS (ngmx) and there are plenty of other bits of visualization software that can replace it. One work-around is simply to "configure --without-x --and-your-other-options" and GROMACS will not attempt to build ngmx, and not require this library for the rest of the installation. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs 4.0 installation problem
Chavatte Philippe wrote: /usr/bin/ld: cannot find -lX11 You don't have X11 installed, probably because you don't need it on a cluster. You can configure --without-x to remove the X11 dependency. -Justin collect2: ld returned 1 exit status make[3]: *** [grompp] Erreur 1 make[3]: quittant le répertoire « /data1/soft/linux/gromacs-4.0s/src/kernel » make[2]: *** [all-recursive] Erreur 1 make[2]: quittant le répertoire « /data1/soft/linux/gromacs-4.0s/src » make[1]: *** [all] Erreur 2 make[1]: quittant le répertoire « /data1/soft/linux/gromacs-4.0s/src » make: *** [all-recursive] Erreur 1 We have compiled gromacs 4.0 on a workstation under RHEL4 without problem. Thank you for your help. P. CHAVATTE - Professeur Philippe CHAVATTE Université Lille 2 Faculté des Sciences Pharmaceutiques et Biologiques Laboratoire de Chimie Thérapeutique - EA1043 BP 83 59006 LILLE CEDEX FRANCE E-Mail : [EMAIL PROTECTED] -- Justin A. Lemkul Graduate Research Assistant 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 listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Gromacs 4.0 installation problem
Hi, We are trying to install gromacs 4.0 on our new SGI cluster running under RHEL5. The configure script run fine (./configure prefix =/install-dir). But an error occurs during the building (make) : cc -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\"/data1/soft/linux/gromacs-4.0/share/top\" -I/data1/soft/linux/fftw-3.1.3/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT grompp.o -MD -MP -MF .deps/grompp.Tpo -c -o grompp.o grompp.c mv -f .deps/grompp.Tpo .deps/grompp.Po /bin/sh ../../libtool --tag=CC --mode=link cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -L/data1/soft/linux/fftw-3.1.3/lib -o grompp grompp.o libgmxpreprocess.la ../mdlib/libmd.la ../gmxlib/libgmx.la -L/usr/lib64 -lnsl -lfftw3f -lm -lX11 cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -o grompp grompp.o -L/data1/soft/linux/fftw-3.1.3/lib ./.libs/libgmxpreprocess.a -L/usr/lib64 ../mdlib/.libs/libmd.a ../gmxlib/.libs/libgmx.a -lnsl /data1/soft/linux/fftw-3.1.3/lib/libfftw3f.a -lm -lX11 /usr/bin/ld: cannot find -lX11 collect2: ld returned 1 exit status make[3]: *** [grompp] Erreur 1 make[3]: quittant le répertoire « /data1/soft/linux/gromacs-4.0s/src/kernel » make[2]: *** [all-recursive] Erreur 1 make[2]: quittant le répertoire « /data1/soft/linux/gromacs-4.0s/src » make[1]: *** [all] Erreur 2 make[1]: quittant le répertoire « /data1/soft/linux/gromacs-4.0s/src » make: *** [all-recursive] Erreur 1 We have compiled gromacs 4.0 on a workstation under RHEL4 without problem. Thank you for your help. P. CHAVATTE - Professeur Philippe CHAVATTE Université Lille 2 Faculté des Sciences Pharmaceutiques et Biologiques Laboratoire de Chimie Thérapeutique - EA1043 BP 83 59006 LILLE CEDEX FRANCE E-Mail : [EMAIL PROTECTED] -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Fatal error, spc.itp", line 41
Chih-Ying Lin wrote: Hi I have the following error and I could not solve it after checking all the possible solutions on line. Thank you Lin --- Program grompp, VERSION 3.3.3 Source code file: toppush.c, line: 1193 Fatal error: [ file "/usr/local/gromacs/share/gromacs/top/spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0). This probably means that you have inserted topology section "settles" in a part belonging to a different molecule than you intended to. In that case move the "settles" section to the right molecule. --- Something in your .top is out of order. Search the archive for the solution; this has been asked several times with regards to spc.itp. -Justin spc.itp, line 41 [ settles ] ; OWfunct doh dhh 1 1 0.1 0.16330 The whole spc.itp file [ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass #ifdef _FF_GROMACS 1 OW 1SOL OW 1 -0.82 2 HW 1SOLHW1 1 0.41 3 HW 1SOLHW2 1 0.41 #endif #ifdef _FF_GROMOS96 #ifdef HEAVY_H 1 OW 1SOL OW 1 -0.829.95140 2 H 1SOLHW1 1 0.414.03200 3 H 1SOLHW2 1 0.414.03200 #else 1 OW 1SOL OW 1 -0.82 15.99940 2 H 1SOLHW1 1 0.411.00800 3 H 1SOLHW2 1 0.411.00800 #endif #endif #ifdef _FF_OPLS 1 opls_116 1SOL OW 1 -0.82 2 opls_117 1SOLHW1 1 0.41 3 opls_117 1SOLHW2 1 0.41 #endif #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.1 345000 0.1 345000 1 3 1 0.1 345000 0.1 345000 [ angles ] ; i j k funct angle force.c. 2 1 3 1 109.47 383 109.47 383 #else [ settles ] ; OWfunct doh dhh 1 1 0.1 0.16330 [ exclusions ] 1 2 3 2 1 3 3 1 2 #endif ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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 listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] tip3p.gro
Chih-Ying Lin wrote: Hi In the file , /usr/local/gromacs/share/gromacs/top/ there is a document named tip3p.itp but there is no tip3p.gro how to create the tip3p.gro Search the archive; this is a frequently asked question. -Justin Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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 listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] tip3p.gro
Hi In the file , /usr/local/gromacs/share/gromacs/top/ there is a document named tip3p.itp but there is no tip3p.gro how to create the tip3p.gro Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fatal error, spc.itp", line 41
Hi I have the following error and I could not solve it after checking all the possible solutions on line. Thank you Lin --- Program grompp, VERSION 3.3.3 Source code file: toppush.c, line: 1193 Fatal error: [ file "/usr/local/gromacs/share/gromacs/top/spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0). This probably means that you have inserted topology section "settles" in a part belonging to a different molecule than you intended to. In that case move the "settles" section to the right molecule. --- spc.itp, line 41 [ settles ] ; OWfunct doh dhh 1 1 0.1 0.16330 The whole spc.itp file [ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass #ifdef _FF_GROMACS 1 OW 1SOL OW 1 -0.82 2 HW 1SOLHW1 1 0.41 3 HW 1SOLHW2 1 0.41 #endif #ifdef _FF_GROMOS96 #ifdef HEAVY_H 1 OW 1SOL OW 1 -0.829.95140 2 H 1SOLHW1 1 0.414.03200 3 H 1SOLHW2 1 0.414.03200 #else 1 OW 1SOL OW 1 -0.82 15.99940 2 H 1SOLHW1 1 0.411.00800 3 H 1SOLHW2 1 0.411.00800 #endif #endif #ifdef _FF_OPLS 1 opls_116 1SOL OW 1 -0.82 2 opls_117 1SOLHW1 1 0.41 3 opls_117 1SOLHW2 1 0.41 #endif #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.1 345000 0.1 345000 1 3 1 0.1 345000 0.1 345000 [ angles ] ; i j k funct angle force.c. 2 1 3 1 109.47 383 109.47 383 #else [ settles ] ; OWfunct doh dhh 1 1 0.1 0.16330 [ exclusions ] 1 2 3 2 1 3 3 1 2 #endif ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] (no subject)
Hi,
In bash, the correct syntax is:
export PATH=$PATH:/usr/local/gromacs/bin
Hope this helps,
Rui Rodrigues
On Wed, 29 Oct 2008 18:52:25 0100 (CET), cecilia.rosso wrote
> Hi! I installed GROMACS on my computer. I try to set up my environment
> adding the line
>
> export PATH "/usr/local/gromacs/bin:${PATH}"
>
> in the .bashrc file, but when I open my terminal, the next message appeared:
>
> bash: export:
> `/usr/local/gromacs/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games':
> not a valid identifier
>
> Why isn't it a valid identifier? What can I do?
>
> The second problem is related to the demo tutorial: when I try to run the
> demo of the folder "tutor/gmxdemo" from the C shell the next message
> appeared:
>
> demo: Command not found.
>
> I don't know if these 2 problems are related each others or if they are
> not. Can you help me, please?
>
> Thank you very much,
> Cecilia Rosso
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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--
Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt)
___
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Re: [gmx-users] (no subject)
Hi Cecilia,
Please give your posts a descriptive title.
Then, this is actually a bash-related issue, which has not much to do
with Gromacs.
But then again, we're nice people :) The thing is that bash wants to have:
export PATH="/usr/local/gromacs/bin:${PATH}"
By the way, you can also use:
source /usr/local/gromacs/bin/GMXRC
which will set the PATH as well as some other relevant environment variables.
Hope it helps,
Tsjerk
On Wed, Oct 29, 2008 at 6:52 PM, <[EMAIL PROTECTED]> wrote:
> Hi! I installed GROMACS on my computer. I try to set up my environment
> adding the line
>
> export PATH "/usr/local/gromacs/bin:${PATH}"
>
> in the .bashrc file, but when I open my terminal, the next message appeared:
>
> bash: export:
> `/usr/local/gromacs/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games':
> not a valid identifier
>
> Why isn't it a valid identifier? What can I do?
>
> The second problem is related to the demo tutorial: when I try to run the
> demo of the folder "tutor/gmxdemo" from the C shell the next message
> appeared:
>
> demo: Command not found.
>
> I don't know if these 2 problems are related each others or if they are
> not. Can you help me, please?
>
> Thank you very much,
> Cecilia Rosso
>
>
>
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
___
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[gmx-users] (no subject)
Hi! I installed GROMACS on my computer. I try to set up my environment
adding the line
export PATH "/usr/local/gromacs/bin:${PATH}"
in the .bashrc file, but when I open my terminal, the next message appeared:
bash: export:
`/usr/local/gromacs/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games':
not a valid identifier
Why isn't it a valid identifier? What can I do?
The second problem is related to the demo tutorial: when I try to run the
demo of the folder "tutor/gmxdemo" from the C shell the next message
appeared:
demo: Command not found.
I don't know if these 2 problems are related each others or if they are
not. Can you help me, please?
Thank you very much,
Cecilia Rosso
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Re: [gmx-users] Re: H2O water density = 6.4617 g/l << 1000 g/l
Chih-Ying Lin wrote: HI As Mark described , "So when you tile these cubes of side length 1.86nm in a 3x3x3 grid, you over-fill a cube of side length 5nm and get 27 water molecules. Use the standard water .gro files in the distribution and then minimize and equilibrate. " And, how could I find the standard water .gro? It is in /share/top/spc216.gro, tip4p.gro, and tip5p.gro, depending on which water model you want to use. -Justin Thank you Lin Here is the 1w.gro 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 3 1SOL OW1.230.628.113 1SOLHW12.137.626.150 1SOLHW23.231.589.021 1.86206 1.86206 1.86206 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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 listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: H2O water density = 6.4617 g/l << 1000 g/l
HI As Mark described , > "So when you tile these cubes of side length 1.86nm in a 3x3x3 grid, you > over-fill a cube of side length 5nm and get 27 water molecules. Use the > standard water .gro files in the distribution and then minimize and > equilibrate. " And, how could I find the standard water .gro? Thank you Lin > Here is the 1w.gro > > 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 > 3 > 1SOL OW1.230.628.113 > 1SOLHW12.137.626.150 > 1SOLHW23.231.589.021 >1.86206 1.86206 1.86206 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] override dispalying of options
On Wed, Oct 29, 2008 at 01:33:19PM +0200, Inon Sharony wrote: > Hello GROMACS users & team > > I would like to run grompp and mdrun from the command line without > having to see all the possible flags and options. I'm running a few > commands in series, so I can't use "grompp &" and then "mdrun &" > Is there some way to call these functions without having to display > all of the (unnecessary) details? hm, how about this? (grompp -blabla > /dev/tty) >& /dev/null but why would you want to run grompp as & ? cheers, marc ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] 1-4 interaction problem with a Thr
Aline Rossi wrote: ;TEMPERATURE COUPLING Tcoupl = berendsen tc-grps = Protein ISZ SOL NA+ tau_t = 0.1 0.1 0.1 0.1 ref_t = 310 310 310 310 This is asking for trouble. See here: http://wiki.gromacs.org/index.php/Thermostats ;table-extension = 1.2 Don't adjust this parameter. The warning you saw is because your system is blowing up: http://wiki.gromacs.org/index.php/blowing_up -Justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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 listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] 1-4 interaction problem with a Thr
Hi group, I'm simulating a protein+drug and always getting the "1-4 interaction between 3013 and 3016 at distance 1.825 which is larger than the 1-4 table size 1.000 nm". These atoms are a CA and a HG1 from a Thr residue. My mdp file is enclosed. What should I encrease or decrease to be able to continue my simulation without this error? Thanks, Aline Rossi ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] 1-4 interaction problem with a Thr
Sorry, I forgot to enclose the .mdp file: ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = PEP MD cpp = /lib/cpp constraints = none integrator = md tinit = 0 dt = 0.002; ps ! nsteps = 50; total 1ns. ;mode for centre of mass motio removal ;comm-mode = linear ;number of steps for centre of mass motion removal nstcomm = 1 nstxout = 5000;output coordinates every 0.5 ps nstvout = 5000; output velocities every 0,5ps nstlog = 5000 nstenergy= 250 nstxtcout= 250 xtc-precision = 1000 ;Selection of energy groups ;NEIGHBORSEARCHING PARAMETERES ;nblist update frequency nstlist = 10 ;ns algorithm (simple or grid) ns_type = grid ;nblist cut-off rlist = 0.9 ;domain-decomposition= no ;OPTIONS FOR ELECTROSTATICS AND VDW ;method for doing electrostatics coulombtype = PME rcoulomb= 0.9 ;method for doing van der waals rvdw= 0.9 ;spacing for the PME FFT grid fourierspacing = 0.12 ;FFT grid size fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ;Ewald/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes constraint_algorithm = lincs lincs_order = 4 ;OPTIONS FOR WEAK COUPLING ALGORITHMS ; Berendsen temperature coupling is off in two groups ;TEMPERATURE COUPLING Tcoupl = berendsen tc-grps = Protein ISZ SOL NA+ tau_t = 0.1 0.1 0.1 0.1 ref_t = 310 310 310 310 ;table-extension = 1.2 ; Energy monitoring ;energygrps = ProteinISZ ; Isotropic pressure coupling is on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 1 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 310 K. gen_vel = yes gen_temp= 310.0 gen_seed= 173529 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] override dispalying of options
And, you can even (like for anything that generates output), redirect output to nowhere: (csh) grompp >& /dev/null (bash) grompp &> /dev/null By the way, bringing it to the background (&) doesn't change the binding to the terminal. Oh, and Mark is absolutely right that it is better to save to a file. Something like (csh): grompp >& log mdrun >>& log & Cheers, Tsjerk On 10/29/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > Inon Sharony wrote: > > > Hello GROMACS users & team > > > > I would like to run grompp and mdrun from the command line without having > to see all the possible flags and options. I'm running a few commands in > series, so I can't use "grompp &" and then "mdrun &" > > Is there some way to call these functions without having to display all of > the (unnecessary) details? > > > > > > Use the -quiet flags with each of them. > > -Justin > > -- > > > Justin A. Lemkul > Graduate Research Assistant > 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 listgmx-users@gromacs.org > http://www.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 [EMAIL PROTECTED] > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] override dispalying of options
Inon Sharony wrote: Hello GROMACS users & team I would like to run grompp and mdrun from the command line without having to see all the possible flags and options. I'm running a few commands in series, so I can't use "grompp &" and then "mdrun &" Is there some way to call these functions without having to display all of the (unnecessary) details? Use the -quiet flags with each of them. -Justin -- Justin A. Lemkul Graduate Research Assistant 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 listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] override dispalying of options
Inon Sharony wrote: Hello GROMACS users & team I would like to run grompp and mdrun from the command line without having to see all the possible flags and options. I'm running a few commands in series, so I can't use "grompp &" and then "mdrun &" Is there some way to call these functions without having to display all of the (unnecessary) details? No. You shouldn't want such a facility. Making multiple commands into a script and saving all of the output into a file is the easiest way of being able to find out exactly what you did after your short-term memory fades. less and grep are probably your friends once you've got that output file. (Or you could make like a real scientist and copy your command lines down longhand into your laboratory notebook ) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] override dispalying of options
Hello GROMACS users & team I would like to run grompp and mdrun from the command line without having to see all the possible flags and options. I'm running a few commands in series, so I can't use "grompp &" and then "mdrun &" Is there some way to call these functions without having to display all of the (unnecessary) details? -- Inon Sharony ינון שרוני +972(3)6407634 atto.TAU.ac.IL/~inonshar Please consider your environmental responsibility before printing this e-mail. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] n terminal
shahrbanoo karbalaee wrote: thank you justin in papers net charge of peptide is calculated +1,with amidated in terminal. that I defined with flag -ter in pdbf2gmx .and when I add tfein system I see in pdb files lys is changed LYSH. OK, so your peptide has a +1 charge. Double check this in your .top (qtot at the last line in the [ atoms ] section). Then just add 1 Cl- in the solvent (probably best to use water) using genion. I've gotten lost as to what the actual problem is any more, but if you have a +1 peptide, it seems clear to me that 1 Cl- belongs in your system. -Justin best -- Justin A. Lemkul Graduate Research Assistant 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 listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: density graph ( density vs time)
huan wrote: Dear Justin and all gmx users, I double checked the density graph (obtained by using g_energy, option 18) which is a energy at y-axis and time at the x-axis. but how can i get a density vs time graph? g_energy defaults to kJ/mol as its unit, but in the case of density it is actually measuring kg/m^3. I don't know if this is a bug or just a default, but in any case, you actually do have density vs. time. -Justin Here i attacthed the graph that i obtained using g_energy. Thank you guys. --- On Wed, 10/29/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: From: Justin A. Lemkul <[EMAIL PROTECTED]> Subject: Re: [gmx-users] density graph ( density vs time) To: "Discussion list for GROMACS users" Date: Wednesday, October 29, 2008, 12:05 AM Jochen Hub wrote: huan wrote: I used g_energy before but i just obtained density (y-axis) versus box length (x axis). huan wrote: Previously i obtained a density (y-axis) versus box length (x axis) using g_density.. Sounds like a contradition to me... :-) Indeed; the g_energy output gives the x-axis as time... -Justin thanks --- On Tue, 10/28/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: From: Justin A. Lemkul <[EMAIL PROTECTED]> Subject: Re: [gmx-users] density graph ( density vs time) To: [EMAIL PROTECTED], "Discussion list for GROMACS users" Date: Tuesday, October 28, 2008, 11:31 PM huan wrote: Dear all, Previously i obtained a density (y-axis) versus box length (x axis) using g_density.. So now i wonder is it there is another way that we can use other way to obtain a density (y axis) versus time length (x-axis). Use g_energy. -Justin Thanks.. --- On Tue, 10/28/08, Mark Abraham <[EMAIL PROTECTED]> wrote: From: Mark Abraham <[EMAIL PROTECTED]> Subject: Re: [gmx-users] density graph ( density vs time) To: "Discussion list for GROMACS users" Date: Tuesday, October 28, 2008, 4:46 PM huan wrote: Dear all gmx-users and developers. I wish to get a density graph with density versus time instead of nm, so how can i obtained this? Please ask a more specific question. We can't tell whether your problem is knowing what tool to use, how to use it, how to label axes of plots or something else. Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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 listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . -- Justin A. Lemkul Graduate Research Assistant 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 listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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 listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Pl
Re: [gmx-users] do_dssp
Morteza Khabiri wrote: Dear florian thanks for your help. I installed the DSSP in the root. It is working well when I run ./dssp in DSSP directory. It seems that the program don't have any problem. As you said I already set an environment also but any of them did not working. It made me crazy that everything is ok, Installing the dssp and also defenition of dssp directory but still i get the previous message. All we can guess is that you haven't done it right. If you want more help, we need more specific information, like what you actually did :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] do_dssp
Dear florian thanks for your help. I installed the DSSP in the root. It is working well when I run ./dssp in DSSP directory. It seems that the program don't have any problem. As you said I already set an environment also but any of them did not working. It made me crazy that everything is ok, Installing the dssp and also defenition of dssp directory but still i get the previous message. thanks ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] table use
Hi, Your apparently have pair interactions in your system. So you have to give the pair interaction table with option -tablep. If the functional shape is the same as the non-bonded interactions, you can just supply the same file name as for the non-bonded tables. Berk > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Date: Tue, 28 Oct 2008 16:55:20 + > Subject: [gmx-users] table use > > Hi all users, > > When I input the mdrun -table table_nonbond.xvg > > it always shows that : > > Fatal error: > Library file tablep.xvg not found in current dir nor in default directories. > (You can set the directories to search with the GMXLIB path variable) > > Has anyone encountered the same problem? Can you share me your experience > about how to solve it ? > > Thank you very much. > > Yang > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] do_dssp
Hi, On Wednesday, 29. October 2008, Morteza Khabiri wrote: > Dear gmx users, > > I run the program do_dssp for my system which is too small. Unfortunately, > I run it for a long time but I am in a doubt that it is working correctly > or not > because it is run for one day and i don't have any idea when it will be > finished and also after running I have a message which said "sh: > /usr/local/bin/dssp: is a directory" Which take me in a doubt that do_dssp > run correctly or not. > > Please give me at least some idea about end time of program. have you installed dssp? do_dssp -h do_dssp reads a trajectory file and computes the secondary structure for each time frame calling the dssp program. If you do not have the dssp program, get it. do_dssp assumes that the dssp executable is /usr/local/bin/dssp. If this is not the case, then you should set an environment variable DSSP pointing to the dssp executable, e.g.: setenv DSSP /opt/dssp/bin/dssp Greetings, Florian -- --- Dr. Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Is it the correct label on Y axis ( density graph)
Mark Abraham wrote: > Jochen Hub wrote: >> huan wrote: >>> Dear all, >>> >>> I am wondering that is it the correct label of y axis in the density >>> graph which i obtained using g_energy? because it is not a density >>> unit but is labeled as kJ/mol >> >> Dear huan, >> >> 1) >> I would encourage you to read a few reviews on MD and the gromacs manual >> carfully. >> >> 2) >> g_energy doesn't write densities, but box vectors which you can use to >> compute your density. > > mdrun calculates densities for simulations with non-constant volume, and > g_energy will show and plot these. Ah, right, I didn't know that (yet :) )! Thanks! Jochen > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > . > -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] do_dssp
Dear gmx users, I run the program do_dssp for my system which is too small. Unfortunately, I run it for a long time but I am in a doubt that it is working correctly or not because it is run for one day and i don't have any idea when it will be finished and also after running I have a message which said "sh: /usr/local/bin/dssp: is a directory" Which take me in a doubt that do_dssp run correctly or not. Please give me at least some idea about end time of program. Thanks, ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Is it the correct label on Y axis ( density graph)
Jochen Hub wrote: huan wrote: Dear all, I am wondering that is it the correct label of y axis in the density graph which i obtained using g_energy? because it is not a density unit but is labeled as kJ/mol Dear huan, 1) I would encourage you to read a few reviews on MD and the gromacs manual carfully. 2) g_energy doesn't write densities, but box vectors which you can use to compute your density. mdrun calculates densities for simulations with non-constant volume, and g_energy will show and plot these. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Is it the correct label on Y axis ( density graph)
huan wrote: > Dear all, > > I am wondering that is it the correct label of y axis in the density graph > which i obtained using g_energy? because it is not a density unit but is > labeled as kJ/mol Dear huan, 1) I would encourage you to read a few reviews on MD and the gromacs manual carfully. 2) g_energy doesn't write densities, but box vectors which you can use to compute your density. Jochen > > Thanks guys. > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > . > -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Is it the correct label on Y axis ( density graph)
huan wrote: Dear all, I am wondering that is it the correct label of y axis in the density graph which i obtained using g_energy? because it is not a density unit but is labeled as kJ/mol It's just an incorrect label. The code writes kJ/mol as the units for all ordinate (i.e. Y-axis) quantities since nobody's troubled to write a mechanism to fix it. You can edit the .xvg file by hand with a text editor to make it look right. g_energy -xvgr allows you to pass in additional lines for output, but I don't know if that will allow you to do anything useful here. The units are probably kg m^-3 Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Is it the correct label on Y axis ( density graph)
Dear all, I am wondering that is it the correct label of y axis in the density graph which i obtained using g_energy? because it is not a density unit but is labeled as kJ/mol Thanks guys. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] n terminal
thank you justin in papers net charge of peptide is calculated +1,with amidated in terminal. that I defined with flag -ter in pdbf2gmx .and when I add tfein system I see in pdb files lys is changed LYSH. best -- sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
