Re: [gmx-users] remd jobs failed

2012-10-19 Thread Davide Mercadante
Hi Albert, Please accept my apologies, I must have misread your e-mail. Effectively everything seems to be right in the command line and I am not able to understand either why you get the error. Good luck. Cheers, Davide On 19/10/12 7:54 PM, "Albert" wrote: >hello David: > >thanks for kind r

Re: [gmx-users] Dipole moment

2012-10-19 Thread Javier Cerezo
When calculated during the md run, the corresponding options in g_energy for the dipole moment are MU-X, MU-Y and MU-Z. However, taking into account the previous mail by David van der Spoel, it's possible that the dipole moment could not be calculated in your system. Options in g_energy vary d

Re: [gmx-users] Dipole moment

2012-10-19 Thread Rajiv Gandhi
Dear Gromacs, I am trying to install gromacs with mpi enabled in my cluster and i end up with following error: libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled argument `../mdlib/libmd_mpi.la' make[1]: *** [libgmxpreprocess_mpi.la] Error I can able to install gromacs i

Re: [gmx-users] Dipole moment

2012-10-19 Thread Chandan Choudhury
Dear Rajiv, Please start a different thread, if you want to get help. I suppose you need to be informative regarding your error(s). Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Oct 19, 2012 at 2:07 PM, Rajiv Gandhi wrote: > Dear Gromacs, > > I am trying to install gromacs with m

Re: [gmx-users] remd jobs failed

2012-10-19 Thread Justin Lemkul
On 10/19/12 2:37 AM, Albert wrote: hello: I am trying to submit replica exchange jobs to cluster by following command, but failed: g_tune_pme_d -x -np 128 mdrun -s remd_.tpr -multi 16 -replex 1000 -reseed -1 -launch Here is the log file: -

[gmx-users] Changing md command line in a script!

2012-10-19 Thread Arman M. Soufiani
Dear all, A simple question. I want to change the md command line in a script. I want to prevent my script to lead the simulation on parallel nodes. By this I mean I want to run it on one CPU. I do not know where I should embed the flag -nt=1 in that command lien. I wonder the following is the md

[gmx-users] Error on mpi installation

2012-10-19 Thread Rajiv Gandhi
Dear Gromacs, I am trying to install gromacs with mpi enabled in my cluster and i end up with following error: libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled argument `../mdlib/libmd_mpi.la' make[1]: *** [libgmxpreprocess_mpi.la] Error I can able to install gromacs i

Re: [gmx-users] Changing md command line in a script!

2012-10-19 Thread Justin Lemkul
On 10/19/12 7:16 AM, Arman M. Soufiani wrote: Dear all, A simple question. I want to change the md command line in a script. I want to prevent my script to lead the simulation on parallel nodes. By this I mean I want to run it on one CPU. I do not know where I should embed the flag -nt=1 in th

[gmx-users] problem with g_density -center

2012-10-19 Thread Christopher Neale
Sorry, Ali, it's not really possible for me to simplify those commands. That's about as simple as it gets. I suggest that you start a normal post that follows the form: I did this (paste commands) and I got this (paste error message). Also, when you get a message like Fatal error: Invalid lin

[gmx-users] problem with g_density -center

2012-10-19 Thread Christopher Neale
Dear Ali: Please also keep in mind that 99% of the papers published with gromacs using NpT have shown density profiles along Z that were computed simply by using (the incorrect) trjconv -center and (the incorrect for NpT) g_density. So while I think that it's always important to get things righ

Re: [gmx-users] Re: Changing md command line in a script!

2012-10-19 Thread Arman Mahboubi Soufiani
Dear Vitaly, I appreciate your informative response. Dear Justin, Thank you for your kind helps. On Fri, Oct 19, 2012 at 5:31 PM, Dr. Vitaly Chaban wrote: > > Dear all, > > > > A simple question. > > I want to change the md command line in a script. I want to prevent my > > script to lead the

Re: [gmx-users] A favor question: experience running Gromacs in the cloud

2012-10-19 Thread Szilárd Páll
Hi, When it comes to hardware, pretty much the only thing that matters is processors (CPUs and maybe GPUs) , memory will always be more than enough -- unless you plan to run massive analysis in the cloud. In general, if your simulation system runs fast enough on a single compute node (1-2 CPUs), t

[gmx-users] problem with g_density -center

2012-10-19 Thread Christopher Neale
My point is that the old paper probably used the incorrect trjconv/g_density as well so to "reproduce" it you may be best off using the standard gromacs. Chris. -- original message -- Thank you so much for your reply but it is very important for me that i can reproduce results of a paper or no

[gmx-users] problem with g_density -center

2012-10-19 Thread Christopher Neale
Sorry Ali, I can't do your work for you. If this is way over your head, then either forget it, find a colleague to help you, or spend some time learning bash and gromacs. I'n not commenting on your approach, but if you modified your .gro then you need a new .top file. You can create one. Chris.

Re: [gmx-users] A favor question: experience running Gromacs in the cloud

2012-10-19 Thread Joris Poort
At Rescale (www.rescale.com) we have cloud-based options for 10Gb/s I/O to run mpi versions of Gromacs. The performance for these has been very good and can scale to hundreds of simulation dynos (computing nodes). Regardless of which service you use, I would highly recommend trying some of the cl

[gmx-users] problem with g_density -center

2012-10-19 Thread Christopher Neale
The solution that I have posted with modified trjconv -center gives the correct values. However, you should always check such things because at the end of the day it is your name on the paper so you are the one responsible. If you want to reproduce a previous result, just contact them to find ou