Re: [gmx-users] Why my system collapsed?

Peggy Yao wrote: Dear all, I've run this simulation twice, but got exactly the same error. Everything was fine up to position restrained simulation. However, the MD simulation was not successful. The final error is: --- Program mdrun, VER

[gmx-users] Why my system collapsed?

Dear all, I've run this simulation twice, but got exactly the same error. Everything was fine up to position restrained simulation. However, the MD simulation was not successful. The final error is: --- Program mdrun, VERSION 3.3.2 Source code f

Re: [gmx-users] Unable to compile Gromacs-CVS because calcpot.c

Thanks David, as you addressed, adding "NULL," at the end of the line 250 of calcpot.c solved the compilation issue. Daniel 2008/4/15 David van der Spoel <[EMAIL PROTECTED]>: > Daniel Adriano Silva M wrote: > > > Hi there, > > > > I am tyring to compile CVS gromacs version "up-to-this-day",

[gmx-users] how to make choices of COM in the system with freeze group

Hi, Users, I have a system with one carbon Nanotube and lots of water, in which Nanotube is frozen. How do I remove the center-of-mass: 1) only remove the COM of SOL 2) remove both COM of SOL and CNT, separately 2) only remove the COM of "system" as a whole. How

[gmx-users] Water flow through Carbon Nanotube

Hello, I am a new user of Gromacs and trying to simulate water flowing in nanotubes. Can I get some idea on how to do this? Where can I have a sample? Thank you very much! Jue Chen Be a better frien

Re: [gmx-users] Minimize error

> --- > Program mdrun, VERSION 3.3.3 > Source code file: nsgrid.c, line: 226 > > Range checking error: > Explanation: During neighborsearching, we assign each particle to a grid > based on its coordinates. If your system contains collisions or par

Re: [gmx-users] Unable to compile Gromacs-CVS because calcpot.c

Daniel Adriano Silva M wrote: Hi there, I am tyring to compile CVS gromacs version "up-to-this-day", and I always finish with the same error (on two different machines), this error is recurrent even if I use gcc or pathscale: edit the file, and on line 250 add at the end "NULL," and recompile

[gmx-users] Minimize error

Hi! I'm trying to minimize a protein into the box filled with solvent. I converted the pdb file into gro file, constructed a triclinic box (volume of ~337 nm3) and filled with 9696 water molecules. I performed the minimization with 15 steps, using steepest descent integrator (mdp file enclo

[gmx-users] Unable to compile Gromacs-CVS because calcpot.c

Hi there, I am tyring to compile CVS gromacs version "up-to-this-day", and I always finish with the same error (on two different machines), this error is recurrent even if I use gcc or pathscale: # cc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/include/libxml2 -I../../include -DGMXLIBDIR=\"/home/

Re: [gmx-users] crash with LINCS WARNING

On Mon, 2008-04-14 at 19:22 -0400, LeeHwan-kyu wrote: > Dear GMX-uers, > > I'm simulating alpha-hemolysin channel in DMPC bilayer and water > (using MARTINI protein FF), and my system keeps crashing with error > below (even with very low timestep). I suspect your problem is the MARTINI protein fo

[gmx-users] make_ndx for separating all atoms in two monolayers in a bilayer

Hi, I want to create an index file which will contain indices of all the atoms in two monolayers separately in a bilayer. For this purpose I have copied a python script from a post in gromacs mailing list, and did a simple modification. But after modification, make_ndx gives me error like "Group 1

Re: [gmx-users] calculating CD spectra

Marieke Schor wrote: Hi, I would like to calculate CD spectra from my simulation input and results (41 amino acid protein simulated in GROMOS or OPLS force field). Apparently this can be done with the MATMAC program (Fleischhauer et al. 1991; Daura et al. 2003). Are there better options (which?)

Re: [gmx-users] xpm2ps help

Quoting "Rigden, LucianeVMello" <[EMAIL PROTECTED]>: > Dear all, > > I am working with gromacs 3.3.3 > > Trying to analyse possible changes in the secondary structure of the peptide > along the simulation. > > do_dssp -f traj.xtc -s topol.tpr -sc -dt 5 > 1 protein I believe the proper analysis sh

Re: [gmx-users] density and CG MARTINI force field

merc mertens wrote: Dear people, I am trying to use the MARTINI CG force field from Marrink et al. for a 100 residue protein in water. I use the tools from the Marrink website (http://md.chem.rug.nl/~marrink/MARTINI/Downloads.html) for preparation of the necessary gro and itp files. For solva

Re: [gmx-users] log file has converted into.log.swp file

Anamika Awasthi wrote: Dear Gromacs Users, Please help me to recover my important log file from swap file, How can I do this? I am wondering wheather I can get my original file or not. Swap file ".md2.log.swp" already exists! [O]pen Read-Only, (E)dit anyway, (R)ecover, (Q)uit: This is wh

Re: [gmx-users] xpm2ps help

Rigden, LucianeVMello wrote: Dear all, I am working with gromacs 3.3.3 Trying to analyse possible changes in the secondary structure of the peptide along the simulation. do_dssp -f traj.xtc -s topol.tpr -sc -dt 5 1 protein xpm2ps -f ss.xpm There are 1 matrices in ss.xpm Matrix 0 is 200

[gmx-users] density and CG MARTINI force field

Dear people, I am trying to use the MARTINI CG force field from Marrink et al. for a 100 residue protein in water. I use the tools from the Marrink website (http://md.chem.rug.nl/~marrink/MARTINI/Downloads.html) for preparation of the necessary gro and itp files. For solvation of my protein I u

[gmx-users] xpm2ps help

Dear all, I am working with gromacs 3.3.3 Trying to analyse possible changes in the secondary structure of the peptide along the simulation. do_dssp -f traj.xtc -s topol.tpr -sc -dt 5 1 protein xpm2ps -f ss.xpm There are 1 matrices in ss.xpm Matrix 0 is 20001 x 12 zsh: segmentation fault

[gmx-users] log file has converted into.log.swp file

Dear Gromacs Users, Please help me to recover my important log file from swap file, How can I do this? I am wondering wheather I can get my original file or not. E325: ATTENTION Found a swap file by the name ".md2.log.swp" owned by: anamika dated: Wed Apr 16 04:21:09 2008 fil

Re: [gmx-users] gromacs analysis performance on a dual core suse box.

Florian Haberl a écrit : Hi, On Tuesday, 15. April 2008 10:15, himanshu khandelia wrote: Hello, I am using a dual core Xeon with 4 GB RAM to do some gromacs analysis and want to know what is the limiting factor in my machine's performance. When I run, say, a trjconv command on a 2.3 GB trajec

Re: [gmx-users] gromacs analysis performance on a dual core suse box.

Hi, On Tuesday, 15. April 2008 10:15, himanshu khandelia wrote: > Hello, > > I am using a dual core Xeon with 4 GB RAM to do some gromacs analysis > and want to know what is the limiting factor in my machine's > performance. > > When I run, say, a trjconv command on a 2.3 GB trajectory, the rest o

[gmx-users] calculating CD spectra

Hi, I would like to calculate CD spectra from my simulation input and results (41 amino acid protein simulated in GROMOS or OPLS force field). Apparently this can be done with the MATMAC program (Fleischhauer et al. 1991; Daura et al. 2003). Are there better options (which?) and if not, could some

[gmx-users] gromacs analysis performance on a dual core suse box.

Hello, I am using a dual core Xeon with 4 GB RAM to do some gromacs analysis and want to know what is the limiting factor in my machine's performance. When I run, say, a trjconv command on a 2.3 GB trajectory, the rest of my machine pretty much freezes up. A trjconv will use only 1 cpu, but is it