Re: [gmx-users] error: Only triclinic boxes...

On 3/06/2011 3:06 AM, Elisabeth wrote: Hello all, I am getting the error below at the very beginning of the simulation (both serial and parallel). I am sure I did not encounter this problem before with the same input files. This has just happened now. I really have no clue why this is

Re: [gmx-users] option -pbc in trjconv

On 3/06/2011 3:42 PM, Kavyashree M wrote: Dear users, I wanted to ensure that the option of -pbc in trjconv is only for visualization, and if I do all possible calculations with the original .xtc file there wont be any problem. -pbc is for any purpose you can think of. Some analyses

Re: [gmx-users] option -pbc in trjconv

Dear Sir, I used dodecahedron for the simulation. My specific doubt was whether do we need to modify the .xtc file using some options of -pbc like nojump, mol, before going for analysis or we can directly go for analysis using the raw .xtc file. Thanking you With regards M. Kavyashree

Re: [gmx-users] option -pbc in trjconv

On 3/06/2011 6:48 PM, Kavyashree M wrote: Dear Sir, I used dodecahedron for the simulation. My specific doubt was whether do we need to modify the .xtc file using some options of -pbc like nojump, mol, before going for analysis or we can directly go for analysis using the raw .xtc file.

[gmx-users] strain

Hi Gromacs users, We would like to apply strain to the system. Is this possible to do with gromacs and if it is how? Thank you in advance, Deniz -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] Solvating dodecahedron

Hi Justin, Note that the pseudo-sphere representation is for visualization purposes only; the triclinic cell should be the input for any simulation. This not true. It doesn't matter which representation you use as input. Molecules may be broken over PBC, but the topological information is

Re: [gmx-users] Solvating dodecahedron

Tsjerk Wassenaar wrote: Hi Justin, Note that the pseudo-sphere representation is for visualization purposes only; the triclinic cell should be the input for any simulation. This not true. It doesn't matter which representation you use as input. Molecules may be broken over PBC, but the

[gmx-users] Combining part files after using -noappend

Hi all, I just discovered nohup for running my simulation without hangup. For some reason using nohup wouldn't except the checksum on my previous md.log file so I just added the -noappend option to create new files. I'm curious, is there a way to combine the part files that emerge from using

Re: [gmx-users] Combining part files after using -noappend

Zack Scholl wrote: Hi all, I just discovered nohup for running my simulation without hangup. For some reason using nohup wouldn't except the checksum on my previous md.log file so I just added the -noappend option to create new files. I'm curious, is there a way to combine the part files

Re: [gmx-users] Is there still interest in rigid-body simulation?

Hi Justin, I added this feature as a new issue under the Gromacs project on Redmine. Recently I also added a Git fork with a very rudimentary version of rigid body code. Let me know if there is anything specific you think I should work on. Thanks a lot, Adam On Thu, Apr 7, 2011 at 12:58 PM,

Re: [gmx-users] gmx4.5.4 installation help

Add --with-pic when configuring fftw. -- Josh On Thu, 2011-06-02 at 15:16 +0800, Jianguo Li wrote: The error message already shows some hints. Try recompile FFTW with -fPIC. Jianguo __ From: Chandan Choudhury

[gmx-users] FFT plan mismatch with mdrun_mpi

Hello, I'll first apologize in case that this is a common issue with an available solution, but I have a problem running mdrun_mpi on a rock cluster and there is no amount of searching that I can do to find information on this error (manual, online docs, general google search). Could someone point

Re: [gmx-users] FFT plan mismatch with mdrun_mpi

On 4/06/2011 3:42 AM, Christian Blouin wrote: Hello, I'll first apologize in case that this is a common issue with an available solution, but I have a problem running mdrun_mpi on a rock cluster and there is no amount of searching that I can do to find information on this error (manual, online

[gmx-users] Re: my apologize

Eli: It was a joke. I want to clarify your relation to Moeed since he asked the SAME question about the compression of the SAME polymer starting from the spring of 2010, but never followed all our advices. Now, you start to ask nearly the SAME questions about absolutely the SAME system. So, I

[gmx-users] Why does the -append option exist?

At first, I thought the -append option of the mdrun command was great. However, I don't think it is anymore and have actually started questioning myself why it exists at the first place, and second, why has it become the default option in the newest versions? It is useless unless you run your

Re: [gmx-users] Why does the -append option exist?

Well sometimes i run out of walltime when doing long simulations and append helps me not to do any file management after restarting simulations from the previous checkpoint. On Fri, Jun 3, 2011 at 3:26 PM, Dimitar Pachov dpac...@brandeis.edu wrote: At first, I thought the -append option of the

[gmx-users] g_rotacf

Hi, I have tried to use g_rotacf to get the rotational autocorrelation plot for a n-h vector, and I have two questions: 1. My MD run is 20ns, but the rotacf.xvg shows only 10ns. why? 2. The plot is bottom out at 500 ps and then go back up. What does it mean physically? Thanks for your insight.

Re: [gmx-users] Why does the -append option exist?

On 4/06/2011 8:26 AM, Dimitar Pachov wrote: At first, I thought the -append option of the mdrun command was great. However, I don't think it is anymore and have actually started questioning myself why it exists at the first place, and second, why has it become the default option in the

Re: [gmx-users] g_rotacf

On 4/06/2011 9:02 AM, simon sham wrote: Hi, I have tried to use g_rotacf to get the rotational autocorrelation plot for a n-h vector, and I have two questions: 1. My MD run is 20ns, but the rotacf.xvg shows only 10ns. why? This can be normal for computed correlation functions. See chapter

Re: [gmx-users] g_rotacf

On 4/06/2011 11:27 AM, Mark Abraham wrote: On 4/06/2011 9:02 AM, simon sham wrote: Hi, I have tried to use g_rotacf to get the rotational autocorrelation plot for a n-h vector, and I have two questions: 1. My MD run is 20ns, but the rotacf.xvg shows only 10ns. why? This can be normal for

[gmx-users] g_rdf problem

Hi, I am using gromacs_4.0.7 to calculate the Scattering Intensity as a function of scattering vectors(q) using g_rdf -sq command . But, I found that there is no way that one can increase/decrease the grid spacing for structure factor calculation. I tried using -bin option , but that does

[gmx-users] Re: Indexing problem when using genconf

Justin A. Lemkul wrote: Ryan S Davis (rsdavis1) wrote: I wanted to copy a bilayer into a grid of 2x2x1 replicas. I used genconf and everything seemed to work fine exept that annoying feature that the command does not reorder the molecule types, so I end up with a .top file looking like

Re: [gmx-users] gmx4.5.4 installation help

Thanks everyone. It helped me in installation. -- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Jun 3, 2011 at 10:36 PM, Joshua L. Phillips jphilli...@ucmerced.edu wrote: Add --with-pic when configuring fftw. -- Josh On Thu, 2011-06-02 at 15:16 +0800, Jianguo Li wrote: The error