Re: [gmx-users] Carbon Nanotube Residue

Justin A. Lemkul wrote: I would recommend reading lots of tutorial material and the Gromacs manual, especially Chapter 5. There are also numerous posts from Chris Stiles that contain a link to a tutorial he set up a while back for doing CNT simulations. I agree, and note that there's some us

Re: [gmx-users] FFTW & Gromacs installation woes on AIX 5.3

Senthil Kumar M wrote: On Thu, Jun 19, 2008 at 12:48 PM, Mark Abraham <[EMAIL PROTECTED]> wrote: Senthil Kumar M wrote: make gives: xlc_r: 1501-224 fatal error in /usr/vac/exe/ipa64: signal 24 received make: 1254-004 The error code from the last command is 251. Stop. make: 1254-004 The error

Re: [gmx-users] FFTW & Gromacs installation woes on AIX 5.3

On Thu, Jun 19, 2008 at 12:48 PM, Mark Abraham <[EMAIL PROTECTED]> wrote: > Senthil Kumar M wrote: >> make gives: >> >> xlc_r: 1501-224 fatal error in /usr/vac/exe/ipa64: signal 24 received >> make: 1254-004 The error code from the last command is 251. >> >> >> Stop. >> make: 1254-004 The error cod

Re: [gmx-users] Carbon Nanotube Residue

I would recommend reading lots of tutorial material and the Gromacs manual, especially Chapter 5. There are also numerous posts from Chris Stiles that contain a link to a tutorial he set up a while back for doing CNT simulations. The main point is that you need to generate a topology that cal

[gmx-users] Carbon Nanotube Residue

I'm new to gromacs and the past week or so I've been digging through the archives so that I can simulate a carbon nanotube. I've been able find coordinates for the carbon nanotube as well as the parameters for the force field. My question is: Do I define the parameters in the force field file or c

Re: [gmx-users] problem with new sugar residue

Hi Carmen, Well, adding a residue to aminoacids.dat only makes sense for amino acids (although I admit to fiddle it sometimes, in which case it is usually best to make a local copy). But one thing with amino acids is that backbone -N(H)-Ca-C(O)- thing, which is referred to in the termini database.

Re: [gmx-users] problem with new sugar residue

Many thanks in advance,but the problem seems to be solved just by not including the new residue name in the aminoacids.dat file, despite the instruction to do so in sec.5.5.1 chapter 5 Topologies of the manual. Can you tell me if this procedure is correct? Thanks again Carmen > Hi Carmen, > > You r

Re: [gmx-users] FFTW & Gromacs installation woes on AIX 5.3

Senthil Kumar M wrote: However, I have included the one instance of error as given below: ./configure --prefix=$HOME/gro333 --disable-largefile --with-fft=fftw2 --disable-fortran followed by make gives: xlc_r: 1501-224 fatal error in /usr/vac/exe/ipa64: signal 24 received make: 1254-004 The

[gmx-users] Re: g_mdmat

Dear gmx-users, I would like to obtain a sample of minimum distance matrices from the trajectory of residues in a protein MD simulation. Obviously, g_mdmat must create this information at some point while generating the contact diagrams, but I would like to extract the real values before

[gmx-users] FFTW & Gromacs installation woes on AIX 5.3

Hi List, We currently have access to a IBM p595 located elsewhere from our lab. I am trying to install Gromacs on it through ssh. I could not install FFTW 3.1.2 but managed to install FFTW 2.1.5. After installing fftw, I followed the installation guidelines (CPPFLAGS etc) and tried to install Gro

RE: [gmx-users] Possible issues with CVS pull code 200800508

Dear Berk (and whoever else might provide assistance) I have included also my topology file topol.tpr at http://drop.io/gmxpull/topol.tpr. From this you can clearly see that there is no pressure coupling in my pulled system. I still have not resolved the issue of the fluctuation artefacts. Berk,

Re: [gmx-users] molecule broken

This is probably a visualization artifact, since mdrun does not make a break bonds to generate fragmented molecules. -Justin Nguyen Hoang Phuong wrote: Dear All, I am running a simulation for a RNA system using 50 cpus with gromacs 3.3.1. At some frames, my molecule is broken, that is parts

[gmx-users] molecule broken

Dear All, I am running a simulation for a RNA system using 50 cpus with gromacs 3.3.1. At some frames, my molecule is broken, that is parts of the molecule are on opposite sides of the periodic box. This problem was reported sometime ago (Nov. 2006) and David suggested to submit the bugzilla.