[gmx-users] g_dist

Title: g_dist Hi all how reacts g_dist if one group contents 3 segments of three identical molecules. Are the distances calculated referring to the centers of mass of the single molecules segments and then averaged or referring to the center of mass of the set of the three segments? Regards

[gmx-users] grompp problem

encountered the problem when running grompp: Fatal error : number of coordinates in coordinate file calsm.pdb,134637 does not match topology cals.top,0 the em.mdp file is as follows : ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; constraints = none integrator = steep

[gmx-users] MD run end abnormally more detailed info

Hi : Mark, thanks for your advice. But i only use the single-processor.And the enviourment is RedHat 9.0 with gromacs 3.3.1. what is other problem of this error Date: Sun, 2 Jul 2006 15:17:53 +1000 (EST)From: "Mark Abraham" [EMAIL PROTECTED]Subject: Re: [gmx-users] MD run end

Re: [gmx-users] grompp problem

Hi, Do you have any temp.top in your folder where you ran genbox? If is yes, you can use it instead of cals.top.[EMAIL PROTECTED] wrote: encountered the problem when running grompp:Fatal error : number of coordinates in coordinate file does not match topology the

Re: [gmx-users] Scripting Analysis tools in tcsh

On Fri, 30 Jun 2006, Arneh Babakhani wrote: Hello GMX users, (this may be more of a tcsh question, but here goes anyway). I'm trying to write a script to go through some trajectories and calculate hbonding. It looks like this: #!/bin/tcsh foreach number (1 2 3 4 5 6 7 8 9 10 11)

Re: [gmx-users] grompp problem

I used the temp.top instead of cals.top and i found the same message : number of coordinates in coordinate file cals.pdb,134637 does not match topology temp.top,0 although the temp.top is not empty. I run gromacs on windows. -- Original Message -- Date: Sun, 2 Jul 2006 09:14:53 -0700 (PDT) From:

[gmx-users] oplsaa force field

Dear GMX users, I'd like to use oplsaa FF format to build my own force field for my project. After I finished it, I can use pdb2gmx. but not grompp. The problem is from my **nb.itp file. I have specified some unusual (not follow the combination rule) nonbonded interaction parameters after [

[gmx-users] LINCS warning

Hi everyone, I'm having trouble with performing 1 ns simulations on a 318 residue long protein with 'mdrun'. The run.log file, included at the end of this message, gives a 'LINCS warning' within a minute or two after the simulation begins: Step 148, time 0.296 (ps) LINCS WARNING relative

Re: [gmx-users] MD run end abnormally more detailed info

Hi : Mark, thanks for your advice. But i only use the single-processor.And the enviourment is RedHat 9.0 with gromacs 3.3.1. OK that should be less problematic. If you are using a single-processor MPI environment, check that you've configured (and started!) that correctly. Preferably try a

Re: [gmx-users] oplsaa force field

The answers to both of these questions are in the comments in src/kernel/toppush.c, in function push_at(). I found them grepping src/*/*.[ch] for scanf (the C function you'd use to read up these files) and looking for topology-related filenames... I'd like to use oplsaa FF format to build my own

Re: [gmx-users] LINCS warning

Hi everyone, I'm having trouble with performing 1 ns simulations on a 318 residue long protein with 'mdrun'. The run.log file, included at the end of this message, gives a 'LINCS warning' within a minute or two after the simulation begins: Step 148, time 0.296 (ps) LINCS WARNING relative

Re: [gmx-users] grompp problem

I didn’t find ccp address in your em.mdp file. Please add ccp.exe to your folder where you will run grompp and add following sentence to em.mdp file cpp = cpp[EMAIL PROTECTED] wrote: I used the temp.top instead of cals.top and i found the same message :number of coordinates in coordinate file

[gmx-users] Hbond dynamic representation in MD movie

Hi all, Is there a tool known for displaying hbonds dynamically during gromacs trajectory visualization process and should also have facility to make MD movie out of it. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A no graphics, no pop-ups email service

Re: [gmx-users] Hbond dynamic representation in MD movie

Hi all, Is there a tool known for displaying hbonds dynamically during gromacs trajectory visualization process and should also have facility to make MD movie out of it. VMD http://www.ks.uiuc.edu/Research/vmd/ Mark ___ gmx-users mailing list

Re: [gmx-users] query about protein-ligand complex

I could not mail you as our net was down, you asked me Is your system properly minimized? My question is how can I understand whether my system is properly minimised? the run is still going on, I can realize that something is going wrong. But I can not detect it.The log file is giving the