Re: [gmx-users] Error message in output file.

coderrr c wrote: Hi, I am trying to run the gromacs and am getting the following error message in the status file.I would like to know what is the significance of the error message,is it going to impact my ouptut???.I am running the mpi version with 6 nodes. p0_2593: p4_error: interr

Re: [gmx-users] what to do if "CU1+" warning appears after grompp?

Stefan Schöbel wrote: Hi, I installed the latest gromacs version but after the grompp command i got this warning that CU1+ is redifined. I tried a new ions.itp that I found in the mailing list but I didn't succeeded. How to solve this problem? Thanks in advance Stefan more info please. whi

Re: [gmx-users] Error message in output file.

coderrr c wrote: Hi, I am trying to run the gromacs and am getting the following error message in the status file.I would like to know what is the significance of the error message,is it going to impact my ouptut???.I am running the mpi version with 6 nodes. p0_2593: p4_error: interr

Re: [gmx-users] Not enough ref_t and tau_t values!

On 10/18/2006 8:10 AM, Aline Rossi wrote: Hi list, Im dealing with a problem when trying to monitoring energygrps. When I run the grompp i receive this output: creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.16# checking input for internal consistency... c

[gmx-users] Error message in output file.

Hi, I am trying to run the gromacs  and  am getting the following error message in the status file.I would like to know what is the significance of the error message,is it going to impact my ouptut???.I am running the mpi version with 6 nodes. p0_2593:  p4_error: interrupt SIGFPE: 8 p3_2608: 

[gmx-users] Not enough ref_t and tau_t values!

Hi list, Im dealing with a problem when trying to monitoring energygrps. When I run the grompp i receive this output: creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.16# checking input for internal consistency... calling /lib/cpp... processing topology... G

[gmx-users] what to do if "CU1+" warning appears after grompp?

Hi, I installed the latest gromacs version but after the grompp command i got this warning that CU1+ is redifined. I tried a new ions.itp that I found in the mailing list but I didn't succeeded. How to solve this problem? Thanks in advance Stefan -- GMX DSL-Flatrate 0,- Euro* - Überall, wo D

Re: [gmx-users] plot rmsd of single atom / residue

Hi,Create an index file with (at least) two groups. One group will be used for fitting the structures (e.g. Calpha atoms), and the other for analysis (e.g. your single atom or residue).Provide this index file to g_rms, select the first group when asked for the fitting group, and the second as the g

Re: [gmx-users] Print out force field contributions in Gromacs

Ugo Cosentino wrote: I want to import in Gromacs a force field I implemented for lanthanide complexes. To test this force field in Gromacs with my previous results, I need to print out at the cycle zero of energy minimization all the stretching, bending etc contributions and parameters. I think

Re: [gmx-users] plot rmsd of single atom / residue

Guenter Fritz wrote: Dear all, I want to extrat a rmsd of a single atom or specific residue from the md trajectory. Should be simple but I didn't dind it. Start with man g_rmsd, and probably then read the manual section on the utility programs. Mark ___

Re: [gmx-users] plot rmsd of single atom / residue

May be you can build an index file which has that specific residue or atom and use it.If not, definitely you can make trajectory with that single atom/ residue and then use g_rmsd to get what you want.I hope its clear. On 10/17/06, Guenter Fritz <[EMAIL PROTECTED]> wrote: Dear Viswanadham,I used g_

Re: [gmx-users] plot rmsd of single atom / residue

Dear Viswanadham, I used g_rmsd but did not find out how to select a single atom or residue. I just got as far as the pre-defined groups in g_rmsd (groups 1-14). Is there something like a a "sub-option" ? You mean you dint find g_rmsd subroutine or you dint know the way to use g_rmsd? On 1

Re: [gmx-users] plot rmsd of single atom / residue

You mean you dint find g_rmsd subroutine or you dint know the way to use g_rmsd?On 10/17/06, Guenter Fritz < [EMAIL PROTECTED]> wrote:Dear all,I want to extrat  a rmsd of a single atom or specific residue from the md trajectory. Should be simple but I didn't dind it.Thanks,Guenter__

[gmx-users] plot rmsd of single atom / residue

Dear all, I want to extrat a rmsd of a single atom or specific residue from the md trajectory. Should be simple but I didn't dind it. Thanks, Guenter ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-us

[gmx-users] Reordering problem AMBER to GROMACS

Hi all gmxers, I'm trying to analyze an amber dynamic (v.8) with the gromacs tools (last version). Sorry in advance for the long message. To do so, I'm trying to generate also a tpr file (needed by some tools). My procedure is being to convert all the MD in multiple pdb format. So I have extracted

[gmx-users] Print out force field contributions in Gromacs

I want to import in Gromacs a force field I implemented for lanthanide complexes. To test this force field in Gromacs with my previous results, I need to print out at the cycle zero of energy minimization all the stretching, bending etc contributions and parameters. I think an output like: bond

Re: [gmx-users] Sanity error in cpp while intalling FFTW

Hi,First, since this is an FFTW-related issue you will probably get better help by asking the FFTW authors.Looking in config.log, the script is trying to preprocess the test program/* confdefs.h.  */#define PACKAGE_NAME "fftw"#define PACKAGE_TARNAME "fftw"#define PACKAGE_VERSION "3.1.2"#define PACK

Fw: [gmx-users] Sanity error in cpp while intalling FFTW

Hi gromacs users,I am trying to install gromacs on Linux. While installing the fftw module , I am getting the following errorat the ./configure stage:[EMAIL PROTECTED] fftw-3.1.2]# ./configure --enable-float --enable-threads --enable-ssechecking for a BSD-

[gmx-users] questions - ED analysis

Hi all, i want to analyze molten globule formation of my protein. so I adopted the protonated states from pka calculations and did MD simulations(10ns) at pH 7 (native), pH3, pH4 and pH2. I did ED analysis to identify the collective motions. 1. Can I use the crystal structure as reference structu

[gmx-users] Sanity error in cpp while intalling FFTW

 Hi gromacs users,I am trying to install gromacs on Linux.  While installing the fftw module , I am getting the following errorat the ./configure stage:[EMAIL PROTECTED] fftw-3.1.2]# ./configure --enable-float --enable-threads --enable-ssechecking for a BSD-compatible install... /usr/bin/install -c

Re: [gmx-users] g_sdf now uploaded to website

Florian Haberl wrote: Hi, On Friday 13 October 2006 09:04, Dallas B. Warren wrote: FYI, g_sdf is now available on the website for download. It generates a spatial distribution function of atom(s) around a reference molecule. It is a radial distribution function in three dimensions, rather tha

Re: [gmx-users] Fatal error: Can't determine precision of trn file, quit!

Prettina Anto_Louis wrote: Hello gromacs users, I ecountered the following error while performing the analysis of the MD run using the tpr and trr files. Select a group: 1 Selected 1: 'Protein' trn version: GMX_trn_file (single precision) Reading frame 830 time 830.000

Re: [gmx-users] how to calculate the shear force(ii)

zzhwise1 wrote: > hi > i didn't say in ditailly about my question in last mail .now i write > it again: >my system is composed of two monolayers,i keep one still and pull the > other one ,and i need to calculated the shear force bettwen them,and the > friction force! but i just have the ed

Re: [gmx-users] How to make a cluster whole

Hi Chris (and others), When doing so, be sure to use a frme which is close enough to the starting frame in terms of the coordinates. -pbc nojump works based on the coordinates and if you use a reference which doesn't match the starting frame close enough everything can get really messed up. Best