Re: [gmx-users] problem with profiling grompp using callgrind

ganapathy senthilkumar wrote: dear gromacs users, i tried to profile the execution of grompp using the callgrind profiling tool. the command is as below. callgrind -v -dump-every-bb = 1000 grompp -f run4.mdp -c run3.gro -p CAVITY2.top -o run4.tpr the program aborted with

Re: [gmx-users] failed dependencies

On Monday 08 May 2006 21:00, David van der Spoel wrote: Jayant James Jayasundar wrote: hi ! I am trying to install GMX on a opteron 2xdual core processor. OS- Suse Linux10.0. I actually installed the intel fortran compiler as I was just not able to get the Suse fortran compiler. I

Re: [gmx-users] problem with profiling grompp using callgrind

this seems more like a bug that is dependent on memory allocation. I'm no aware of any known bug in grompp. Maybe you can recompile all of grompp with the -g flag and retry. For memory debugging simpler tools like Electric Fence usually work. For profiling, you'd probably want to profile

Re: [gmx-users] problem with profiling grompp using callgrind

Berk Hess wrote: this seems more like a bug that is dependent on memory allocation. I'm no aware of any known bug in grompp. Maybe you can recompile all of grompp with the -g flag and retry. For memory debugging simpler tools like Electric Fence usually work. For profiling, you'd probably

[gmx-users] Speptide - mdrun failed

Dear All, I'm just getting started with GROMACS. I configured and installed fftw-3.0.1 and then I configured, compiled and installed gromacs-3.3.1.tar.gz as INSTALL file showed. I thought that the installation had been successful and I performed the simulation of the peptide (speptide, the one

Re: [gmx-users] problem with profiling grompp using callgrind

From: David van der Spoel [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] problem with profiling grompp using callgrind Date: Tue, 09 May 2006 09:36:36 +0200 Berk Hess

[gmx-users] Value for bonded force constant (Kb)

Dear gmxions, Could any one give me the value for bonded force constant (Kb) to be used for restraining ,F(II) and ligating atoms of proteins ( 2 HISs and 1 ASP)using harmonic potential (type 6). With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm -

Re: [gmx-users] Speptide - mdrun failed

[EMAIL PROTECTED] wrote: Dear All, I'm just getting started with GROMACS. I configured and installed fftw-3.0.1 and then I configured, compiled and installed gromacs-3.3.1.tar.gz as INSTALL file showed. I thought that the installation had been successful and I performed the simulation of the

[gmx-users] grompp error on nanotube

-- Aina Quintillá Institut fuer Nanotechnologie Forschungszentrum Karlsruhe Tel: +49 (0) 7247 82 6360 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests

[gmx-users] Fatal error: moleculetype SOL is redefined.

Hi gromaxers, I want to generate a tpr file for a minimization. I have 3 peptides in water and Im using OPLS ff, but after I run grompp, system backs me the next message: -- creating statusfile for 1 node... checking input for internal consistency... calling

[gmx-users] Fatal error: moleculetype SOL is redefined.

Hi gromaxers, I want to generate a tpr file for a minimization. I have 3 peptides in water and Im using OPLS ff, but after I run grompp, system backs me the next message: -- creating statusfile for 1 node... checking input for internal consistency... calling

Re: [gmx-users] Value for bonded force constant (Kb)

raja wrote: Dear gmxions, Could any one give me the value for bonded force constant (Kb) to be used for restraining ,F(II) and ligating atoms of proteins ( 2 HISs and 1 ASP)using harmonic potential (type 6). Find a paper that does a similar thing and base your construction on

Re: [gmx-users] Fatal error: moleculetype SOL is redefined.

Absalom Zamorano wrote: Strangely enough, the problem is here: Fatal error: moleculetype SOL is redefined Find where moleculetype SOL is defined in your .top file - perhaps implicitly through an #include - and you should see it defined more than once. Evidently you can't do this :-) Mark

[gmx-users] Segmentation fault in disco

Hi all, I tried to perform a CONCOORD simulation by means of cdist and disco routines included in GROMACS. However, while cdist appears to work well, disco produces a segmentation fault error. Maybe a problem in managing memory? Does anybody give me a clue? Thanks in advance! -- Fabrizio

Re: [gmx-users] Segmentation fault in disco

Fabrizio Mancinelli wrote: Hi all, I tried to perform a CONCOORD simulation by means of cdist and disco routines included in GROMACS. However, while cdist appears to work well, disco produces a segmentation fault error. Maybe a problem in managing memory? Does anybody give me a clue? Thanks in

[gmx-users] Water near protein

Hi I have a protein that I have simulated for 1 ns. I want to observe the variation in the number of water molecules within 2.0 A of the backbone of the protein, as a function of time. So I should be able to see this variation as a graph in xmgrace, with time on the X axis, and the number

[gmx-users] g_angle gets confused by switching default output file names.

g_angle -ov angaver.xvg :: yields average angle g_angle -ov angdist.xvg :: yields angle distribution My Gromacs-3.3 command was: g_angle -ov x.xvg -type dihedral -f traj.xtc -s topol.tpr -n my.ndx Easily avoided, just posting a notice. ___ gmx-users

Re: [gmx-users] Water near protein

Ashutosh Jogalekar wrote: Hi I have a protein that I have simulated for 1 ns. I want to observe the variation in the number of water molecules within 2.0 A of the backbone of the protein, as a function of time. So I should be able to see this variation as a graph in xmgrace, with time on