[gmx-users] trjorder

2013-03-12 Thread Nidhi Katyal
Dear all I would like to know the number of oxygen atoms of my co-solvent molecules which are around 0.3nm of the protein in the last few ns. I have read the manual and found that trjorder could serve the purpose. So i have first created index file containing all the oxygen atoms of my co-solvent m

[gmx-users] Re: combine two gro files

2013-03-12 Thread shika
Thanks Dr. Dallas for your replying. But my friend told me that the extended one is only 2 ns not the total 22ns. So,the gro for the extended one is not affect at all? I thought that the gro file that prodice from the extend one is only 2 ns. Thanks Doc! On Wed, Mar 13, 2013 at 11:19 AM, Dalla

RE: [gmx-users] combine two gro files

2013-03-12 Thread Dallas Warren
Why is it that you want to combine the two coordinate files? md.gro is the coordinates of the system at the end of 20ns. md_extend.gro is the coordinates of the system at the end of 22ns. So combining them will not make much sense. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Inst

[gmx-users] Postdoc jobs developing gromacs etc.

2013-03-12 Thread David van der Spoel
If you are interested in a gromacs-related development position at the postdoc level, please have a look at our ad below. Please spread to interested colleagues. http://www.uu.se/jobb/others/annonsvisning?languageId=1&tarContentId=235221 Regards, -- David van der Spoel, Ph.D., Professor of Bio

RE: [gmx-users] mdrun WARING and crash

2013-03-12 Thread L.Liu
Hallo Justin, One update on the wired snapshot mentioned on previous email. I checked over the output coordinates and xmgrace it with xy directions, finding that it is not crystal, instead it is a normal homogeneous box. All these give us a clue that it might be the trajectory file goes wrong, c

Re: [gmx-users] Mismatching number of PP MPI processes and GPUs per node

2013-03-12 Thread George Patargias
Hi Carsten Thanks a lot for this tip. It worked! George > Hi, > > On Mar 11, 2013, at 10:50 AM, George Patargias wrote: > >> Hello >> >> Sorry for posting this again. >> >> I am trying to run GROMACS 4.6 compiled with MPI and GPU acceleration >> (CUDA 5.0 lib) using the following SGE batch scri

Re: [gmx-users] Gromacs with Intel Xeon Phi coprocessors ?

2013-03-12 Thread Szilárd Páll
Hi Chris, You should be able to run on MIC/Xeon Phi as these accelerators, when used in symmetric mode, behave just like a compute node. However, for two main reasons the performance will be quite bad: - no SIMD accelerated kernels for MIC; - no accelerator-specific parallelization implemented (as

[gmx-users] No default U-B types

2013-03-12 Thread 라지브간디
Dear gmx users. I have specified the bond line for heme with CO ligand in specbond.dat and it created topology with special bond in bond type. However, when i come to the steps of atomic-level description of our system in the binary file using ions.tpr, i got an following error. ERROR 1 [

[gmx-users] constant velocity pulling/Umbrella sampling

2013-03-12 Thread raghav singh
Hello Fellow Users, I have a doubt about the mdp option in case of constant velocity pulling / Umbrella pulling simulation. pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N N Y pull_start = yes ; define initial COM distance >

Re: [gmx-users] setting the gromacs 4.6.1 path

2013-03-12 Thread Mark Abraham
On Tue, Mar 12, 2013 at 11:14 AM, 라지브간디 wrote: > dear gmx. > > > i am having a problem of setting the path as mentioned in gromacs manual > 4.6.1 version. > > > I used > > > source /usr/local/gromacs/bin/GMXRC > > > bash: goto: command not found.. > What is your terminal? What is its version? Yo

[gmx-users] setting the gromacs 4.6.1 path

2013-03-12 Thread 라지브간디
dear gmx. i am having a problem of setting the path as mentioned in gromacs manual 4.6.1 version. I used source /usr/local/gromacs/bin/GMXRC bash: goto: command not found.. when i use echo "source /usr/local/gromacs/bin/GMXRC" >> ~/.bash_profile it work on that terminal only. cant a

Re: [gmx-users] query for gromacs-4.5.4

2013-03-12 Thread Mark Abraham
It could be anything. But until we see some GROMACS diagnostic messages, nobody can tell. Mark On Tue, Mar 12, 2013 at 10:08 AM, Chaitali Chandratre wrote: > Sir, > > Thanks for your reply > But the same script runs on some other cluster with apprx same > configuration but not on cluster on

RE: [gmx-users] mdrun WARING and crash

2013-03-12 Thread L.Liu
Hallo Justin, Thank you for your reply, I uploaded the images, Please find following the link below, start box: http://s1279.beta.photobucket.com/user/Li_Liu/media/image0_zpsf95d10fe.jpeg.html?filters[user]=134822327&filters[recent]=1&filters[publicOnly]=1&sort=1&o=1 and snapshot for first ste

Re: [gmx-users] query for gromacs-4.5.4

2013-03-12 Thread Chaitali Chandratre
Sir, Thanks for your reply But the same script runs on some other cluster with apprx same configuration but not on cluster on which I am doing set up. Also job hangs after some 16000 steps but not come out immediately. It might be problem with configuration or what? Thanks... Chaitali On T

Re: [gmx-users] query for gromacs-4.5.4

2013-03-12 Thread Mark Abraham
They're just MPI error messages and don't provide any useful GROMACS diagnostics. Look in the end of the .log file, stderr and stdout for clues. One possibility is that your user's system is too small to scale effectively. Below about 1000 atoms/core you're wasting your time unless you've balanced