Re: [gmx-users] Regarding g_densmap output
On Fri, Aug 30, 2013 at 11:18 AM, Venkat Reddy venkat...@gmail.com wrote: Dear Gromacs users, I am analyzing the density of my spherical lipid vesicle using g_densmap tool with the following options. g_densmap -f vesicle_noPBC.xtc -s vesicle-12us.tpr -n index.ndx -dt 1000 -od -amax 6 -rmax 6 -mirror I am getting densmap.dat as output, which is a text file. How to analyze this text file? Also Please suggest me any tool which can convert this text file to some visually appealing grid map or a 2D (or) 3D graph? use xpm2ps. Thanks for your valuable time -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Issue in ligand gyration analysis
Nitin, You can use g_polystat and see if you can reproduce your observations. Chandan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] analysis tool of 407 to 46x
Dear gmx users,
I have calculated the bonded distibutions of a polymer melt by writing an
analysis tool (template.c). The tool was written in gmx 4.0.7 version.
code snippet
* do {
/* coordinates are available in the vector fr.x
* you can find this and all other structures in
* the types directory under the gromacs include dir.
* Note how flags determines wheter to read x/v/f!
*/
for(i = 0; i top.atoms.nr;) {
dist = distance(fr.x[i][XX], fr.x[i + 1][XX],\
fr.x[i][YY], fr.x[i + 1][YY],\
fr.x[i][ZZ], fr.x[i + 1][ZZ]);
histogram(dist, hist_AB[0]);
i = i + 9;
}
} while(read_next_frame(status,fr));
for(i = 1; i maxbin; i++)
fprintf(fdistAB,%f %f\n, (i-1)*delr, hist_AB[i]);
float distance(float xi, float xj, float yi, float yj, float zi, float zj)
{
float dist = 0.0;
dist = sqrt(pow((xi - xj), 2) + pow((yi - yj), 2) + pow((zi - zj),
2));
return (dist);
}
int histogram(float dist, float *hist)
{
int bin = 0;
bin = (int)(dist/delr) + 1;
if(bin maxbin)
{
hist[bin] = hist[bin] + 1;
}
return 0;
}
*
**
Now, I want to import the code to the latest version (4.6.x). I find that
the structure of template is different. Can anyone guide me ?
Also, I want to implement the following lines in the template. How can this
be done?
*for(i = 0; i top.atoms.nr; i++){
fprintf(fw,ATOM %5d %-4s OW %4d%8.3f%8.3f%8.3f\n,\
i,*(top.atoms.atomname[i]),top.atoms.atom[i].resnr,
fr.x[i][XX]*10,
fr.x[i][YY]*10, fr.x[i][ZZ]*10);
}
*
Any suggestions would b every helpful.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
--
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Re: [gmx-users] Tutor directory in gromacs 4.6
There are no such directory. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Jun 12, 2013 at 1:56 PM, colinbannister colin.bannis...@nottingham.ac.uk wrote: Hope I'm not missing something obvious here - but I can't find the 'share/tutor' directory in my Gromacs 4.6 installation. Should it be there ? thanks, Colin -- View this message in context: http://gromacs.5086.x6.nabble.com/Tutor-directory-in-gromacs-4-6-tp5009078.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Unable to download Gromacs source tar file
I too cannot download (tried with 3.3 4.5.5 4.6 and 4.5.7). Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Sat, Jun 8, 2013 at 4:05 PM, Mark Abraham mark.j.abra...@gmail.comwrote: They're still fine. There must be a problem at your end, I'm afraid. Mark On Sat, Jun 8, 2013 at 10:46 AM, Bhamy Maithry Shenoy bhamymait...@aero.iisc.ernet.in wrote: Hi, Thanks for your reply. But the problem still persists. Even now I am not able to download. -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Fri 6/7/2013 8:14 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Unable to download Gromacs source tar file They're fine now. Perhaps the FTP server was offline briefly. Mark On Fri, Jun 7, 2013 at 7:41 AM, Bhamy Maithry Shenoy bhamymait...@aero.iisc.ernet.in wrote: Hi, I would like to use Gromacs for MD simulation of biomolecules. But I am not able to download any of the source files from the link http://www.gromacs.org/Downloads Can anyone please help. Thanks and regards, Maithry -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GPU problem
Hi Albert, I think using -nt flag (-nt=16) with mdrun would solve your problem. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Jun 4, 2013 at 12:56 PM, Albert mailmd2...@gmail.com wrote: Dear: I've got four GPU in one workstation. I am trying to run two GPU job with command: mdrun -s md.tpr -gpu_id 01 mdrun -s md.tpr -gpu_id 23 there are 32 CPU in this workstation. I found that each job trying to use the whole CPU, and there are 64 sub job when these two GPU mdrun submitted. Moreover, one of the job stopped after short of running, probably because of the CPU issue. I am just wondering, how can we distribute CPU when we run two GPU job in a single workstation? thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] ngmx not installed in gmx4.6.1
Dear gmx users, I had installed gromacs 4.6.1 using cmake. All the binaries are installed, but surprisingly I do not find ngmx executable. Can anyone guide me how do I install ngmx using cmake. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] ngmx not installed in gmx4.6.1
Thanks David. It worked. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Jun 5, 2013 at 1:02 AM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: I do not know about the newest versions, but in older ones ngmx was missed when you did not have the lesstif library installed. Dr. Vitaly Chaban On Tue, Jun 4, 2013 at 5:55 PM, Chandan Choudhury iitd...@gmail.com wrote: Dear gmx users, I had installed gromacs 4.6.1 using cmake. All the binaries are installed, but surprisingly I do not find ngmx executable. Can anyone guide me how do I install ngmx using cmake. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] nstxout, nstvout, . . .
You need to re submit the jobs, with decreased time. -- Chandan kumar Choudhury NCL, Pune INDIA On Sat, Apr 6, 2013 at 11:20 AM, dina dusti dinadu...@yahoo.com wrote: Dear Specialists I am a beginner at Gromacs. I work with MARTINI CG force field. I selected 5 for nstxout= 5 nstvout= 5 nstenergy= 5 nstlog= 5 nstxtcout= 5 and my jobs have been finished. I found that this time is very large. Is there a way for correct this time? Or, should I do these jobs again?! May I ask you to help me, Please? Best Regards Dina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] no CUDA-capable device is detected
On Thu, Mar 28, 2013 at 2:41 PM, Berk Hess g...@hotmail.com wrote: Hi, The code compiled, so the compiler is not the issue. I guess mdrun picked up GPU 0, which it should have ignored. You only want to use GPU 1. Could you try running: mdrun -ntmpi 1 -gpu_id 1 $mdrun_461 -ntmpi 1 -gpu_id 1 -s md0-25.tpr Note: file tpx version 73, software tpx version 83 NOTE: Error occurred during GPU detection: no CUDA-capable device is detected Can not use GPU acceleration, will fall back to CPU kernels. No GPUs detected --- Program mdrun_461, VERSION 4.6.1 Source code file: /home/sudip/RPMs/gromacs-4.6.1/src/gmxlib/gmx_detect_hardware.c, line: 580 Fatal error: Some of the requested GPUs do not exist, behave strangely, or are not compatible: GPU #1: inexistent Cheers, berk Date: Thu, 28 Mar 2013 10:51:58 +0200 Subject: Re: [gmx-users] no CUDA-capable device is detected From: g...@bioacademy.gr To: gmx-users@gromacs.org Hi Chandan Are you using the same version of GCC compiler that you used to compile CUDA 5.0? In my hands, gcc 4.7.2 could not compile CUDA 5.0 (I think there was some kind of incompatibility between the two). There is an work around with gcc 4.7.2. Please see http://svshift.blogspot.in/2013/03/running-nvidai-cuda-sdk-50-on-opensuse.html Can you try compiling both CUDA 5.0 and GROMACS with gcc 4.6.1? This worked in my system (MacOS/Darwin). Just make sure to set the variables CC and CXX to point to the right compiler version when you run cmake. George Dear GMX Users, I am trying to execute Gromacs 4.6.1 on one of the GPU server: *OS*: OpenSuse 12.3 x86_64 3.7.10-1.1-desktop (Kernel Release) *gcc*: 4.7.2 CUDA Library paths #CUDA-5.0 export CUDA_HOME=/usr/local/cuda-5.0 export PATH=$CUDA_HOME/bin:$PATH export LD_LIBRARY_PATH=$CUDA_HOME/lib64:/lib:$LD_LIBRARY_PATH The gromacs has been compiled with CMAKE_PREFIX_PATH=/opt/apps/fftw-3.3.3/single:/usr/local/cuda-5.0 cmake .. -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/opt/apps/gromacs/461/single -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_461 -DGMX_LIBS_SUFFIX=_461 -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda *Error on executing mdrun * * * *NOTE: Error occurred during GPU detection: no CUDA-capable device is detected Can not use GPU acceleration, will fall back to CPU kernels. Will use 24 particle-particle and 8 PME only nodes This is a guess, check the performance at the end of the log file Using 32 MPI threads No GPUs detected *I checked my cuda installation. I am able to compile and execute the sample programmes e.g., deviceQuery. Also executed *nvidia-smi *: +--+ | NVIDIA-SMI 4.310.40 Driver Version: 310.40 | |---+--+--+ | GPU Name | Bus-Id Disp. | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===+==+==| | 0 NVS 300 | :03:00.0 N/A | N/A | | N/A 49C N/A N/A / N/A | 3% 16MB / 511MB | N/A Default | +---+--+--+ | 1 Tesla K20c | :04:00.0 Off | Off | | 30% 38C P8 16W / 225W | 0% 13MB / 5119MB | 0% Default | +---+--+--+ +-+ | Compute processes: GPU Memory | | GPU PID Process name Usage | |=| | 0 Not Supported | +-+ What am I missing that Gromacs is not detecting the GPUs. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
Re: [gmx-users] no CUDA-capable device is detected
On Thu, Mar 28, 2013 at 4:09 PM, Szilárd Páll szilard.p...@cbr.su.sewrote: Hi, If mdrun says that it could not detect GPUs it simply means that the GPU enumeration found no GPUs, otherwise it would have printed what was found. This is rather strange because mdrun uses the same mechanism the deviceQuery SDK example. I really don't have a good idea what could be the issue, but you could try recompiling or compiling with CUDA 4.2 to see if any of that makes a difference. Let us know if you figured out something. Cheers, Thanks Szilárd for the eye opening comment. I just tried running gromacs as root. I recalled I had executed deviceQuery as root. While executing as user it produces the same error : */root/NVIDIA_CUDA-5.0_Samples/1_Utilities/deviceQuery/deviceQuery Starting... CUDA Device Query (Runtime API) version (CUDART static linking) cudaGetDeviceCount returned 38 - no CUDA-capable device is detected* Now, running gromacs as root, it is running successfully (I suppose). Output of nvidia-smi +--+ | NVIDIA-SMI 4.310.40 Driver Version: 310.40 | |---+--+--+ | GPU Name | Bus-IdDisp. | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===+==+==| | 0 NVS 300 | :03:00.0 N/A | N/A | | N/A 48C N/A N/A / N/A | 3% 17MB / 511MB | N/A Default | +---+--+--+ | 1 Tesla K20c | :04:00.0 Off | Off | | 50% 62CP0 106W / 225W | 2% 87MB / 5119MB | 76% Default | +---+--+--+ +-+ | Compute processes: GPU Memory | | GPU PID Process name Usage | |=| |0Not Supported | |1 9127 mdrun_461 72MB | +-+ Output of md.log 2 GPUs detected: #0: NVIDIA Tesla K20c, compute cap.: 3.5, ECC: no, stat: compatible #1: NVIDIA NVS 300, compute cap.: 1.2, ECC: no, stat: incompatible 1 GPU auto-selected for this run: #0 I think there is something relate to permissions. Though nvcc has 755 permission, something else might require additional permissions. Chandan -- Szilárd On Thu, Mar 28, 2013 at 2:39 AM, Berk Hess g...@hotmail.com wrote: Hi, I am not the expert on GPU detection, so we'll need to wait until an expert replies. Maybe GPU 0 is ignored and the GPUs are renumbered, could you try: mdrun -ntmpi 1 -gpu_id 0 Also your tpr file is from an older version. It will not run on a GPU. You need to set the mdp option: cutoff-scheme = Verlet and run grompp to get a new tpr file. Cheers, Berk From: iitd...@gmail.com Date: Thu, 28 Mar 2013 14:57:16 +0530 Subject: Re: [gmx-users] no CUDA-capable device is detected To: gmx-users@gromacs.org On Thu, Mar 28, 2013 at 2:41 PM, Berk Hess g...@hotmail.com wrote: Hi, The code compiled, so the compiler is not the issue. I guess mdrun picked up GPU 0, which it should have ignored. You only want to use GPU 1. Could you try running: mdrun -ntmpi 1 -gpu_id 1 $mdrun_461 -ntmpi 1 -gpu_id 1 -s md0-25.tpr Note: file tpx version 73, software tpx version 83 NOTE: Error occurred during GPU detection: no CUDA-capable device is detected Can not use GPU acceleration, will fall back to CPU kernels. No GPUs detected --- Program mdrun_461, VERSION 4.6.1 Source code file: /home/sudip/RPMs/gromacs-4.6.1/src/gmxlib/gmx_detect_hardware.c, line: 580 Fatal error: Some of the requested GPUs do not exist, behave strangely, or are not compatible: GPU #1: inexistent Cheers, berk Date: Thu, 28 Mar 2013 10:51:58 +0200 Subject: Re: [gmx-users] no CUDA-capable device is detected From: g...@bioacademy.gr To: gmx-users@gromacs.org Hi Chandan Are you using the same version of GCC compiler that you used to compile CUDA 5.0? In my hands, gcc 4.7.2 could not compile CUDA 5.0 (I think there was some kind of incompatibility between the two). There is an work around with gcc 4.7.2. Please see http://svshift.blogspot.in/2013/03/running-nvidai-cuda-sdk-50-on-opensuse.html Can you try compiling both CUDA 5.0 and GROMACS with gcc 4.6.1? This
Re: [gmx-users] no CUDA-capable device is detected
Hi !! I problem with the permission of /dev/nvidia* changed it to 0666 /dev/nvidia* Everything resolved. mdrun can be executed as normal user. Thanks everyone. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Mar 28, 2013 at 4:26 PM, Chandan Choudhury iitd...@gmail.comwrote: On Thu, Mar 28, 2013 at 4:09 PM, Szilárd Páll szilard.p...@cbr.su.sewrote: Hi, If mdrun says that it could not detect GPUs it simply means that the GPU enumeration found no GPUs, otherwise it would have printed what was found. This is rather strange because mdrun uses the same mechanism the deviceQuery SDK example. I really don't have a good idea what could be the issue, but you could try recompiling or compiling with CUDA 4.2 to see if any of that makes a difference. Let us know if you figured out something. Cheers, Thanks Szilárd for the eye opening comment. I just tried running gromacs as root. I recalled I had executed deviceQuery as root. While executing as user it produces the same error : */root/NVIDIA_CUDA-5.0_Samples/1_Utilities/deviceQuery/deviceQuery Starting... CUDA Device Query (Runtime API) version (CUDART static linking) cudaGetDeviceCount returned 38 - no CUDA-capable device is detected* Now, running gromacs as root, it is running successfully (I suppose). Output of nvidia-smi +--+ | NVIDIA-SMI 4.310.40 Driver Version: 310.40 | |---+--+--+ | GPU Name | Bus-IdDisp. | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===+==+==| | 0 NVS 300 | :03:00.0 N/A | N/A | | N/A 48C N/A N/A / N/A | 3% 17MB / 511MB | N/A Default | +---+--+--+ | 1 Tesla K20c | :04:00.0 Off | Off | | 50% 62CP0 106W / 225W | 2% 87MB / 5119MB | 76% Default | +---+--+--+ +-+ | Compute processes: GPU Memory | | GPU PID Process name Usage | |=| |0Not Supported | |1 9127 mdrun_461 72MB | +-+ Output of md.log 2 GPUs detected: #0: NVIDIA Tesla K20c, compute cap.: 3.5, ECC: no, stat: compatible #1: NVIDIA NVS 300, compute cap.: 1.2, ECC: no, stat: incompatible 1 GPU auto-selected for this run: #0 I think there is something relate to permissions. Though nvcc has 755 permission, something else might require additional permissions. Chandan -- Szilárd On Thu, Mar 28, 2013 at 2:39 AM, Berk Hess g...@hotmail.com wrote: Hi, I am not the expert on GPU detection, so we'll need to wait until an expert replies. Maybe GPU 0 is ignored and the GPUs are renumbered, could you try: mdrun -ntmpi 1 -gpu_id 0 Also your tpr file is from an older version. It will not run on a GPU. You need to set the mdp option: cutoff-scheme = Verlet and run grompp to get a new tpr file. Cheers, Berk From: iitd...@gmail.com Date: Thu, 28 Mar 2013 14:57:16 +0530 Subject: Re: [gmx-users] no CUDA-capable device is detected To: gmx-users@gromacs.org On Thu, Mar 28, 2013 at 2:41 PM, Berk Hess g...@hotmail.com wrote: Hi, The code compiled, so the compiler is not the issue. I guess mdrun picked up GPU 0, which it should have ignored. You only want to use GPU 1. Could you try running: mdrun -ntmpi 1 -gpu_id 1 $mdrun_461 -ntmpi 1 -gpu_id 1 -s md0-25.tpr Note: file tpx version 73, software tpx version 83 NOTE: Error occurred during GPU detection: no CUDA-capable device is detected Can not use GPU acceleration, will fall back to CPU kernels. No GPUs detected --- Program mdrun_461, VERSION 4.6.1 Source code file: /home/sudip/RPMs/gromacs-4.6.1/src/gmxlib/gmx_detect_hardware.c, line: 580 Fatal error: Some of the requested GPUs do not exist, behave strangely, or are not compatible: GPU #1: inexistent Cheers, berk Date: Thu, 28 Mar 2013 10:51:58 +0200 Subject: Re: [gmx-users] no CUDA-capable device is detected From: g...@bioacademy.gr To: gmx-users@gromacs.org Hi Chandan Are you using the same version of GCC compiler that you used to compile CUDA
[gmx-users] no CUDA-capable device is detected
Dear GMX Users, I am trying to execute Gromacs 4.6.1 on one of the GPU server: *OS*: OpenSuse 12.3 x86_64 3.7.10-1.1-desktop (Kernel Release) *gcc*: 4.7.2 CUDA Library paths #CUDA-5.0 export CUDA_HOME=/usr/local/cuda-5.0 export PATH=$CUDA_HOME/bin:$PATH export LD_LIBRARY_PATH=$CUDA_HOME/lib64:/lib:$LD_LIBRARY_PATH The gromacs has been compiled with CMAKE_PREFIX_PATH=/opt/apps/fftw-3.3.3/single:/usr/local/cuda-5.0 cmake .. -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/opt/apps/gromacs/461/single -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_461 -DGMX_LIBS_SUFFIX=_461 -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda *Error on executing mdrun * * * *NOTE: Error occurred during GPU detection: no CUDA-capable device is detected Can not use GPU acceleration, will fall back to CPU kernels. Will use 24 particle-particle and 8 PME only nodes This is a guess, check the performance at the end of the log file Using 32 MPI threads No GPUs detected *I checked my cuda installation. I am able to compile and execute the sample programmes e.g., deviceQuery. Also executed *nvidia-smi *: +--+ | NVIDIA-SMI 4.310.40 Driver Version: 310.40 | |---+--+--+ | GPU Name | Bus-Id Disp. | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===+==+==| | 0 NVS 300 | :03:00.0 N/A | N/A | | N/A 49C N/A N/A / N/A | 3% 16MB / 511MB | N/A Default | +---+--+--+ | 1 Tesla K20c | :04:00.0 Off | Off | | 30% 38C P8 16W / 225W | 0% 13MB / 5119MB | 0% Default | +---+--+--+ +-+ | Compute processes: GPU Memory | | GPU PID Process name Usage | |=| | 0 Not Supported | +-+ What am I missing that Gromacs is not detecting the GPUs. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] re: .HTP FILE
Hi Boopathi, Adding hydrogen atoms to the hdb is explained in the sectio 5.6.4 of gromacs manual 4.5.4. Please refer the manual. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Jan 10, 2013 at 11:32 AM, Subramaniam Boopathi boopathi...@gmail.com wrote: Dear All I have created the pdb file for interaction of protein with new molecules. I am able to rum the pdb file successfully but I am facing error in the Equillibration process. The Error shows that *atom HAQ is missing in residue NIC 8 in the pdb file You might need to add atom HAQ to the hydrogen database of building block NIC in the file aminoacids.hdb (see the manual) * likewise 14 atoms H atoms are missing in residu*e.Can anyone help me how to add atom in .htp file for new molecules interacting with protein.Thanks in advance. with regards Boopathi.s * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Index file
On Mon, Dec 31, 2012 at 11:59 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Dear all, I had a .pdb file containing protein, popc, and ions. So I used editconf to make a .gro file. But when I want to make an index file, 2 CL ions are not identified, so I can not choose it. use make_ndx f .pdb Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Index file
On Mon, Dec 31, 2012 at 1:07 PM, Chandan Choudhury iitd...@gmail.comwrote: On Mon, Dec 31, 2012 at 11:59 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Dear all, I had a .pdb file containing protein, popc, and ions. So I used editconf to make a .gro file. But when I want to make an index file, 2 CL ions are not identified, so I can not choose it. use make_ndx f .pdb use make_ndx -f .pdb Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Chandan kumar Choudhury NCL, Pune INDIA -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_tune_pme for multiple nodes
Dear Carsten and Florian, Thanks for you useful suggestions. It did work. I still have a doubt regarding the execution : export MPIRUN=`which mpirun` export MDRUN=/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5 g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log I am suppling $NPROCS as 24 [2 (nodes)*12(ppn)], so that g_tune_pme tunes the no. of pme nodes. As I am executing it on a single node, mdrun never checks pme for greater than 12 ppn. So, how do I understand that the pme is tuned for 24 ppn spanning across the two nodes. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Nov 29, 2012 at 8:32 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Chandan, On Nov 29, 2012, at 3:30 PM, Chandan Choudhury iitd...@gmail.com wrote: Hi Carsten, Thanks for your suggestion. I did try to pass to total number of cores with the np flag to the g_tune_pme, but it didnot help. Hopefully I am doing something silliy. I have pasted the snippet of the PBS script. #!/bin/csh #PBS -l nodes=2:ppn=12:twelve #PBS -N bilayer_tune cd $PBS_O_WORKDIR export MDRUN=/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5 from here on you job file should read: export MPIRUN=`which mpirun` g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log mpirun -np $NPROCS g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 this way you will get $NPROCS g_tune_pme instances, each trying to run an mdrun job on 24 cores, which is not what you want. g_tune_pme itself is a serial program, it just spawns the mdrun's. Carsten Then I submit the script using qsub. When I login to the compute nodes there I donot find and mdrun executable running. I also tried using nodes=1 and np 12. It didnot work through qsub. Then I logged in to the compute nodes and executed g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 It worked. Also, if I just use $g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 g_tune_pme executes on the head node and writes various files. Kindly let me know what am I missing when I submit through qsub. Thanks Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Sep 3, 2012 at 3:31 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Chandan, g_tune_pme also finds the optimal number of PME cores if the cores are distributed on multiple nodes. Simply pass the total number of cores to the -np option. Depending on the MPI and queue environment that you use, the distribution of the cores over the nodes may have to be specified in a hostfile / machinefile. Check g_tune_pme -h on how to set that. Best, Carsten On Aug 28, 2012, at 8:33 PM, Chandan Choudhury iitd...@gmail.com wrote: Dear gmx users, I am using 4.5.5 of gromacs. I was trying to use g_tune_pme for a simulation. I intend to execute mdrun at multiple nodes with 12 cores each. Therefore, I would like to optimize the number of pme nodes. I could execute g_tune_pme -np 12 md.tpr. But this will only find the optimal PME nodes for single nodes run. How do I find the optimal PME nodes for multiple nodes. Any suggestion would be helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten
Re: [gmx-users] g_tune_pme for multiple nodes
Hi Carsten, Thanks for the reply. If PME nodes for the g_tune is half of np, then if it exceeds the ppn of of a node, how would g_tune perform. What I mean if $NPROCS=36, the its half is 18 ppn, but 18 ppns are not present in a single node (max. ppn = 12 per node). How would g_tune function in such scenario? Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Dec 4, 2012 at 6:39 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Chandan, the number of separate PME nodes in Gromacs must be larger than two and smaller or equal to half the number of MPI processes (=np). Thus, g_tune_pme checks only up to npme = np/2 PME nodes. Best, Carsten On Dec 4, 2012, at 1:54 PM, Chandan Choudhury iitd...@gmail.com wrote: Dear Carsten and Florian, Thanks for you useful suggestions. It did work. I still have a doubt regarding the execution : export MPIRUN=`which mpirun` export MDRUN=/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5 g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log I am suppling $NPROCS as 24 [2 (nodes)*12(ppn)], so that g_tune_pme tunes the no. of pme nodes. As I am executing it on a single node, mdrun never checks pme for greater than 12 ppn. So, how do I understand that the pme is tuned for 24 ppn spanning across the two nodes. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Nov 29, 2012 at 8:32 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Chandan, On Nov 29, 2012, at 3:30 PM, Chandan Choudhury iitd...@gmail.com wrote: Hi Carsten, Thanks for your suggestion. I did try to pass to total number of cores with the np flag to the g_tune_pme, but it didnot help. Hopefully I am doing something silliy. I have pasted the snippet of the PBS script. #!/bin/csh #PBS -l nodes=2:ppn=12:twelve #PBS -N bilayer_tune cd $PBS_O_WORKDIR export MDRUN=/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5 from here on you job file should read: export MPIRUN=`which mpirun` g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log mpirun -np $NPROCS g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 this way you will get $NPROCS g_tune_pme instances, each trying to run an mdrun job on 24 cores, which is not what you want. g_tune_pme itself is a serial program, it just spawns the mdrun's. Carsten Then I submit the script using qsub. When I login to the compute nodes there I donot find and mdrun executable running. I also tried using nodes=1 and np 12. It didnot work through qsub. Then I logged in to the compute nodes and executed g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 It worked. Also, if I just use $g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 g_tune_pme executes on the head node and writes various files. Kindly let me know what am I missing when I submit through qsub. Thanks Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Sep 3, 2012 at 3:31 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Chandan, g_tune_pme also finds the optimal number of PME cores if the cores are distributed on multiple nodes. Simply pass the total number of cores to the -np option. Depending on the MPI and queue environment that you use, the distribution of the cores over the nodes may have to be specified in a hostfile / machinefile. Check g_tune_pme -h on how to set that. Best, Carsten On Aug 28, 2012, at 8:33 PM, Chandan Choudhury iitd...@gmail.com wrote: Dear gmx users, I am using 4.5.5 of gromacs. I was trying to use g_tune_pme for a simulation. I intend to execute mdrun at multiple nodes with 12 cores each. Therefore, I would like to optimize the number of pme nodes. I could execute g_tune_pme -np 12 md.tpr. But this will only find the optimal PME nodes for single nodes run. How do I find the optimal PME nodes for multiple nodes. Any suggestion would be helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users
Re: [gmx-users] g_tune_pme for multiple nodes
On Tue, Dec 4, 2012 at 7:18 PM, Carsten Kutzner ckut...@gwdg.de wrote: On Dec 4, 2012, at 2:45 PM, Chandan Choudhury iitd...@gmail.com wrote: Hi Carsten, Thanks for the reply. If PME nodes for the g_tune is half of np, then if it exceeds the ppn of of a node, how would g_tune perform. What I mean if $NPROCS=36, the its half is 18 ppn, but 18 ppns are not present in a single node (max. ppn = 12 per node). How would g_tune function in such scenario? Typically mdrun allocates the PME and PP nodes in an interleaved way, meaning you would end up with 9 PME nodes on each of your two nodes. Check the -ddorder of mdrun. Interleaving is normally fastest unless you could have all PME processes exclusively on a single node. Thanks Carsten for the explanation. Chandan Carsten Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Dec 4, 2012 at 6:39 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Chandan, the number of separate PME nodes in Gromacs must be larger than two and smaller or equal to half the number of MPI processes (=np). Thus, g_tune_pme checks only up to npme = np/2 PME nodes. Best, Carsten On Dec 4, 2012, at 1:54 PM, Chandan Choudhury iitd...@gmail.com wrote: Dear Carsten and Florian, Thanks for you useful suggestions. It did work. I still have a doubt regarding the execution : export MPIRUN=`which mpirun` export MDRUN=/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5 g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log I am suppling $NPROCS as 24 [2 (nodes)*12(ppn)], so that g_tune_pme tunes the no. of pme nodes. As I am executing it on a single node, mdrun never checks pme for greater than 12 ppn. So, how do I understand that the pme is tuned for 24 ppn spanning across the two nodes. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Nov 29, 2012 at 8:32 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Chandan, On Nov 29, 2012, at 3:30 PM, Chandan Choudhury iitd...@gmail.com wrote: Hi Carsten, Thanks for your suggestion. I did try to pass to total number of cores with the np flag to the g_tune_pme, but it didnot help. Hopefully I am doing something silliy. I have pasted the snippet of the PBS script. #!/bin/csh #PBS -l nodes=2:ppn=12:twelve #PBS -N bilayer_tune cd $PBS_O_WORKDIR export MDRUN=/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5 from here on you job file should read: export MPIRUN=`which mpirun` g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log mpirun -np $NPROCS g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 this way you will get $NPROCS g_tune_pme instances, each trying to run an mdrun job on 24 cores, which is not what you want. g_tune_pme itself is a serial program, it just spawns the mdrun's. Carsten Then I submit the script using qsub. When I login to the compute nodes there I donot find and mdrun executable running. I also tried using nodes=1 and np 12. It didnot work through qsub. Then I logged in to the compute nodes and executed g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 It worked. Also, if I just use $g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 g_tune_pme executes on the head node and writes various files. Kindly let me know what am I missing when I submit through qsub. Thanks Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Sep 3, 2012 at 3:31 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Chandan, g_tune_pme also finds the optimal number of PME cores if the cores are distributed on multiple nodes. Simply pass the total number of cores to the -np option. Depending on the MPI and queue environment that you use, the distribution of the cores over the nodes may have to be specified in a hostfile / machinefile. Check g_tune_pme -h on how to set that. Best, Carsten On Aug 28, 2012, at 8:33 PM, Chandan Choudhury iitd...@gmail.com wrote: Dear gmx users, I am using 4.5.5 of gromacs. I was trying to use g_tune_pme for a simulation. I intend to execute mdrun at multiple nodes with 12 cores each. Therefore, I would like to optimize the number of pme nodes. I could execute g_tune_pme -np 12 md.tpr. But this will only find the optimal PME nodes for single nodes run. How do I find the optimal PME nodes for multiple nodes. Any suggestion would be helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive
Re: [gmx-users] g_tune_pme for multiple nodes
Hi Carsten, Thanks for your suggestion. I did try to pass to total number of cores with the np flag to the g_tune_pme, but it didnot help. Hopefully I am doing something silliy. I have pasted the snippet of the PBS script. #!/bin/csh #PBS -l nodes=2:ppn=12:twelve #PBS -N bilayer_tune cd $PBS_O_WORKDIR export MDRUN=/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5 mpirun -np $NPROCS g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 Then I submit the script using qsub. When I login to the compute nodes there I donot find and mdrun executable running. I also tried using nodes=1 and np 12. It didnot work through qsub. Then I logged in to the compute nodes and executed g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 It worked. Also, if I just use $g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 g_tune_pme executes on the head node and writes various files. Kindly let me know what am I missing when I submit through qsub. Thanks Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Sep 3, 2012 at 3:31 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Chandan, g_tune_pme also finds the optimal number of PME cores if the cores are distributed on multiple nodes. Simply pass the total number of cores to the -np option. Depending on the MPI and queue environment that you use, the distribution of the cores over the nodes may have to be specified in a hostfile / machinefile. Check g_tune_pme -h on how to set that. Best, Carsten On Aug 28, 2012, at 8:33 PM, Chandan Choudhury iitd...@gmail.com wrote: Dear gmx users, I am using 4.5.5 of gromacs. I was trying to use g_tune_pme for a simulation. I intend to execute mdrun at multiple nodes with 12 cores each. Therefore, I would like to optimize the number of pme nodes. I could execute g_tune_pme -np 12 md.tpr. But this will only find the optimal PME nodes for single nodes run. How do I find the optimal PME nodes for multiple nodes. Any suggestion would be helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Dipole moment
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 graji...@gmail.com wrote: 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 in single precision without having trouble. However, when i use mpi enabled by using lam-7.4.1 it gives above mentioned error, I have tried openmpi also but its not even compile it and ends up with error like configure: error: cannot compute sizeof (off_t) I have used the command line ./configure --program-suffix=_mpi --enable-mpi --enable-shared I do not know how to solve this problem. Any suggestion would be much appreciated. Regards Rajiv On Fri, Oct 19, 2012 at 4:17 PM, Javier Cerezo j...@um.es wrote: 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 depending on the actual computation. If you want to calculate the dipole moment by your own, I think it's easier to use the xtc file exported every 3fs (it'll be considerably heavier than the edr file, however) and writing an specific code for your purposes. In order to read the trajectories, you can use the xtc library ( http://www.gromacs.org/**Developer_Zone/Programming_**Guide/XTC_Libraryhttp://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library). Anyway, if the code didn't compute it, there should be a reason. Javier El 19/10/12 04:42, Nilesh Dhumal escribió: Is it possible to calcualte the dipole moment at 3fs by modifing the source code? Nilesh How can I save the total dipole moment extacted by .edr file? I could not find the option in g_energy. Nilesh Justin is right. I've slipped a bit, that was not the way to set nstenergy. But still, you can save the dipole directly in the edr file. Not from your existing trajectory, but in a new run. Say your dt=1fs, then you should set nstenergy=3 to get your dipole moment every 3fs which you can retrieve with g_energy. Javier El 18/10/12 20:43, Nilesh Dhumal escribió: In short, I can not save dipole moment directly. I can calculate dipole moment only using .trr file. Nilesh On 10/18/12 1:45 PM, Javier Cerezo wrote: Hi The dipole is stored in the edr file, which output frequency is controlled by nstenergy option in the mdp parameter file. Set it appropriately during your run (nstenergy=0.003) but keep in mind that it should be a multiple of the time step. nstenergy cannot be set this way; it is an integer indicating the interval (in number of steps) for writing energy values. If the values have been saved every 2 ps, there is no way to retrieve them every 3 fs; if more frequent information is needed, it needs to be saved more frequently. -Justin El 18/10/12 18:09, Nilesh Dhumal escribió: Hello, I am calculating the dipole moment auto-correlation function for my system which have 128 cation and 128 anion. I am saving the trajectory at each 2 ps and using this trajectory for further analysis. Can I save the dipole moment and three vectors at each 3 fs? Thanks Nilesh -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting!
[gmx-users] g_tune_pme for multiple nodes
Dear gmx users, I am using 4.5.5 of gromacs. I was trying to use g_tune_pme for a simulation. I intend to execute mdrun at multiple nodes with 12 cores each. Therefore, I would like to optimize the number of pme nodes. I could execute g_tune_pme -np 12 md.tpr. But this will only find the optimal PME nodes for single nodes run. How do I find the optimal PME nodes for multiple nodes. Any suggestion would be helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_tune_pme optimal PME nodes for multiple nodes
Dear gmx users, I am using 4.5.5 of gromacs. I was trying to use g_tune_pme for a simulation. I intend to execute mdrun at multiple nodes with 12 cores each. Therefore, I would like to optimize the number of pme nodes. I could execute g_tune_pme -np 12 md.tpr. But this will only find the optimal PME nodes for single nodes run. How do I find the optimal PME nodes for multiple nodes. Any suggestion would be helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] xtc file and trr file
On Fri, Aug 17, 2012 at 2:16 PM, Acoot Brett acootbr...@yahoo.com wrote: Dear All, After a production MD, both the xtc file and trr file are produced. trr file is much larger than the xtc file. But when we openned the original gro file one of the file from xtc file and trr file in VMD, we will find the xtc contains more frames in comparison with the trr file. Will you please explain why xtc file is smaller file than the trr file, but the xtc file contains more frames in VMD? http://www.gromacs.org/Documentation/File_Formats/Trajectory_File I am looking forward to getting your reply. Cheers, Acoot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem regarding installation of gromacs-4.5.5
Nidhi, To get reply from the gmx community, you need to post the error messages which erupts while compiling. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Jun 18, 2012 at 11:43 AM, Nidhi Jatana nidhijat...@bic-svc.ac.inwrote: Dear Sir/Madam Thanks for all the help. I have removed the older version of gromacs and the new one also and hve reinstalled gromacs again. But I am still encountering the same problem. I am unable to figure out. First I removed the installed gromacs and all the links. The set of commands that I have given to install gromacs are as folllows: * ./configure --enable-mpi --program-suffix=_mpi make make mdrun -j 8 make install make install-mdrun make links export PATH=$PATH:/usr/local/gromacs/bin/GMXRC echo $PATH* Please note that initially I had problems while compiling gromacs so I reinstalled fftw (version 3.3.2) by giving in the following commands: *cd fftw-3.3.2 ./configure --enable-float --enable-sse --enable-shared make make install* Please help. I am unable to figure out what's wrong with the installation. Thanking you Regards -- Nidhi Jatana Senior Research Fellow Bioinformatics Center Sri Venkateswara College (University of Delhi) Dhaula Kuan New Delhi-110021. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem regarding installation of gromacs-4.5.5
Ok. You need to source the GMXRC file Follow http://www.gromacs.org/Documentation/Installation_Instructions For bash shell: if your executables are in /usr/local/gromacs/bin $source /usr/local/gromacs/bin/GMXRC Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Jun 18, 2012 at 11:54 AM, Nidhi Jatana nidhijat...@bic-svc.ac.in wrote: Dear Sir/Madam I am not getting any errors while compiling. Its all running fine. Thanking you Regards -- Nidhi Jatana Senior Research Fellow Bioinformatics Center Sri Venkateswara College (University of Delhi) Dhaula Kuan New Delhi-110021. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] mdrun -v output
Dear gmx users, Is it possible to redirect the output of mdrun -v to a file while submitting the job using pbs script? mdrun -v -s md.tpr verbose.txt donot produce output (to file verbose.txt) while the job is running. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun -v output
On Mon, Jun 18, 2012 at 12:43 PM, Javier Cerezo j...@um.es wrote: Information messages, such as those shown on the screen during mdrun are output to stderr. So if you want to get them you should redirect as follows: mdrun -v -s md.tpr 2 verbose.txt In the case where you may need to get all output (from both stdout and stderr) you should use: mdrun -v -s md.tpr verbose.txt Thanks. It is actually mdrun -v -s md.tpr verbose.txt Javier El 18/06/12 08:49, Chandan Choudhury escribió: Dear gmx users, Is it possible to redirect the output of mdrun -v to a file while submitting the job using pbs script? mdrun -v -s md.tpr verbose.txt donot produce output (to file verbose.txt) while the job is running. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun -v output
Thanks Peter for the clarification. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Jun 19, 2012 at 2:27 AM, Peter C. Lai p...@uab.edu wrote: It actually depends on your shell/environment :-P On sun grid engine and derivatives, the you can have the scheduler capture the stdout and stderr output through the -o and -e parameters, respectively. On 2012-06-18 05:28:11PM +0530, Chandan Choudhury wrote: On Mon, Jun 18, 2012 at 12:43 PM, Javier Cerezo j...@um.es wrote: Information messages, such as those shown on the screen during mdrun are output to stderr. So if you want to get them you should redirect as follows: mdrun -v -s md.tpr 2 verbose.txt In the case where you may need to get all output (from both stdout and stderr) you should use: mdrun -v -s md.tpr verbose.txt Thanks. It is actually mdrun -v -s md.tpr verbose.txt Javier El 18/06/12 08:49, Chandan Choudhury escribió: Dear gmx users, Is it possible to redirect the output of mdrun -v to a file while submitting the job using pbs script? mdrun -v -s md.tpr verbose.txt donot produce output (to file verbose.txt) while the job is running. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] analysing of the long trajectories
trjconv -dt use dt flag with the utility trjconv Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Jun 15, 2012 at 12:07 PM, a a pat...@hotmail.com wrote: try ptraj -- Date: Fri, 15 Jun 2012 10:18:40 +0400 Subject: Re: [gmx-users] analysing of the long trajectories From: jmsstarli...@gmail.com To: gmx-users@gromacs.org By the way, I'm also looking for a most trivial way for extraction of pdb files from my trajectory on the desired intervals. E.g I have trajectory consisted of 5000 frames and I want to obtain 10 pdb files every each 500 frames ( or selected time interval as the alternative ). Commonly I do it manually via VMD ( save pdb option) but is there any automatic way to do it expecially for a long trajectories? James -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb to xyz file format
Use editconf http://manual.gromacs.org/current/online/editconf.html Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Sun, Jun 10, 2012 at 11:30 PM, Matthias Ernst matthias.ern...@student.kit.edu wrote: Why do you want to use Gromacs? I would suggest to use openBabel, which can convert a whole bunch of file formats... Regards, Matthias Am 10.06.2012 16:55, schrieb Lara Bunte: Hi Is it possible to convert a .pdb file to a .xyz file with GROMACS? At this point there shouldn't be a force field or final topology, I just want to convert this formats to each other. Is it possible with GROMACS? Greetings Lara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding gromacs manual.
On Thu, May 24, 2012 at 10:39 AM, Seera Suryanarayana paluso...@gmail.comwrote: Dear all gromacs users, I am new for MD and in particular using gromacs software.I would like to learn basics of gromacs.Please tell me the name of the manual which one is suitable for me. http://www.gromacs.org/@api/deki/files/152/=manual-4.5.4.pdf Chandan Suryanarayana Seera, PhD student, Hyderabad, India. -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] extending a simulation after it get stopped because of queue time limit
On Sat, Feb 25, 2012 at 12:09 PM, priya thiyagarajan priya.thiyagaraja...@gmail.com wrote: hello sir, i was performing simulation for 30ns. due to queue time limit my mdrun stopped at 11.6ns.. then i extended my simulation using these two commands *tpbconv -s md.tpr -extend 2 -o newmd.tpr * I suppose you donot need to extend as the information to execute for 30ns is contained in the md.tpr. What you need to is to just include -cpi state.cpt while resubmitting your job. i.e., *mdrun -s md.tpr -cpi state.cpt **-o md.trr -c md.gro -e md.edr -g md.log **-x traj.xtc* * * * * Chandan * mdrun -s newmd.tpr -o md.trr -c md.gro -e md.edr -g md.log -cpi state.cpt -x traj.xtc -append * when i submit my mdrun i got error as Output file appending has been requested, but some output files listed in the checkpoint file state.cpt are not present or are named differently by the current program: output files present: md.log md.trr md.edr output files not present or named differently: traj.xtc --- Program mdrun, VERSION 4.5.5 Source code file: checkpoint.c, line: 2146 Fatal error: File appending requested, but only 3 of the 4 output files are present For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors but i had traj.xtc file in my folder.. then again i checked my folder and again submitted my job.. this time i got different error.. i dono why i am getting like this... i got error as Reading file newmd.tpr, VERSION 4.5.5 (single precision) Starting 8 threads Reading checkpoint file state.cpt generated: Fri Feb 17 19:46:58 2012 --- Program mdrun, VERSION 4.5.5 Source code file: checkpoint.c, line: 1757 Fatal error: Failed to lock: md.log. Function not implemented. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors same command i used but i got different errors each time.. can anyone please help me with your answer.. i searched in users list.. but i didnt get the point.. please help with your answer. thanking you, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] getting rid of PBC, completely
On Thu, Jan 19, 2012 at 3:49 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Chandan, The box is accessible from the t_trxframe struct. Assuming you have t_trxframe *fr You can access it through fr-box Thanks Tsjerk. It (fr.box) did help me to get the box coordinates. fr.box[XX][XX], fr.box[YY][YY] and fr.box[ZZ][ZZ] gives me the values but fr.box[XX][YY], fr.box[XX][ZZ] prints 0. Which seems to me that the origin of the box is at (0,0,0). Then, fr.box[XX][XX] is the maximum X-coordinate, fr.box[YY][YY] is the maximum Y-coordinate,fr.box[ZZ][ZZ] is the maximum Z-coordinate. Am I correct? But if you remove jumps first, you're fine anyway. Just don't put things back in the box afterwards. And don't center if your aim is calculating MSDs. Yeah, you are right. Chandan Hope it helps, Tsjerk On Thu, Jan 19, 2012 at 11:14 AM, Chandan Choudhury iitd...@gmail.com wrote: On Thu, Jan 19, 2012 at 12:17 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 19/01/2012 5:39 PM, Chandan Choudhury wrote: Dear gmx-users, I have a simulated a system containing a linear polymer in a cubic box with water molecules. I need to get rid of PBC effect on the system such that I can execute my own analysis code. I intend to compute the msd of water molecules along the polymer backbone. You can't get rid of PBC, you can only manage it. The question reduces what you want to see if a molecule diffuses across the periodic boundary from near one end of the polymer to the other end. So, when I execute my own analysis code, I see the msd's are abrupt (i.e very high), this is due to the pbc. So, for getting rid of PBC effect, I performed the suggested trjconv workflow ( http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions ). Below are my executed commands : # Made the system whole echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc whole -o 0-4_whole.xtc # 0 is the whole system. md0-4.tpr is the initial tpr file containing whole (no broken) polymer inside the cubic box. # Extracted 1st frame from the initial trajectory echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc nojump -o 1st.pdb -dump 0 # used the whole trajectory to remove jumps with reference to the 1st frame. echo 0 | trjconv_4.5.5 -s 1st.pdb -f 0-4_whole.xtc -pbc nojump -o 0-4_nojump.xtc So here you said let molecules diffuse away from the solute. #system is being centered echo 0 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4_nojump.xtc -o 0-4_center.xtc -center #putting every atom in the box echo 0 | trjconv -s md0-4.tpr -f 0-4_center.xtc -o 0-4_box.xtc -pbc atom ... and now you said take all the atoms and put them back in the box, creating jumps whenever one crosses the boundaries. Still when I execute my analysis code, I do see the abrupt behaviour in the msd plot. Can someone guide me how to completely get rid of PBC artifacts. Don't simulate with them :-P Is your analysis technique sound for the periodic case? No, my analysis code doesnot take care of PBC. As to deal with PBC, I need to have the box vectors (for atleast NPT simulation) from the trajectory and I am unable to extract the box vectors (as of date). Chandan Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support
[gmx-users] getting rid of PBC, completely
Dear gmx-users, I have a simulated a system containing a linear polymer in a cubic box with water molecules. I need to get rid of PBC effect on the system such that I can execute my own analysis code. I intend to compute the msd of water molecules along the polymer backbone. So, when I execute my own analysis code, I see the msd's are abrupt (i.e very high), this is due to the pbc. So, for getting rid of PBC effect, I performed the suggested trjconv workflow ( http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions ). Below are my executed commands : # Made the system whole echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc whole -o 0-4_whole.xtc # 0 is the whole system. md0-4.tpr is the initial tpr file containing whole (no broken) polymer inside the cubic box. # Extracted 1st frame from the initial trajectory echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc nojump -o 1st.pdb -dump 0 # used the whole trajectory to remove jumps with reference to the 1st frame. echo 0 | trjconv_4.5.5 -s 1st.pdb -f 0-4_whole.xtc -pbc nojump -o 0-4_nojump.xtc #system is being centered echo 0 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4_nojump.xtc -o 0-4_center.xtc -center #putting every atom in the box echo 0 | trjconv -s md0-4.tpr -f 0-4_center.xtc -o 0-4_box.xtc -pbc atom Still when I execute my analysis code, I do see the abrupt behaviour in the msd plot. Can someone guide me how to completely get rid of PBC artifacts. Chadan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] box vectors
On Thu, Dec 8, 2011 at 12:33 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 8/12/2011 2:54 PM, Chandan Choudhury wrote: Thanks everyone for the responses. I should have framed my question much more precisely. I am trying to use the template.c code of (gmx_4.0.7) and within this, I want to take care of PBC. To do this, I should be having the knowledge of box dimensions. How can this done? Check out the code of g_bond or g_dist to see how to get access to the box information from the trajectory, and how that might be used. Note that it's important to get the data from the trajectory frame rather than the .tpr when the former varies, and I am not sure that the code of those tools does this correctly at the moment, or in 4.0.7 (see http://redmine.gromacs.org/issues/834). Mark Thanks Mark for the response. I did look at the code of g_hbond and g_dist. Truly speaking, I couldnot decode any information from it. Actually, I dont have such a broad knowledge in C. Can some one point me out what functions/variables should be called in template.c (gmx_4.0.7) to obtain the box vectors. Chandan I also know that the g_energy prints the box vector with the simulation time. But, trjconv -dump also writes the box vectors in the pdb file. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Dec 8, 2011 at 3:33 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 8/12/2011 4:36 AM, Chandan Choudhury wrote: Dear gmx_users, I am using gmx_4.0.7. I need to print the box vectors from the trajectory of a simulated system. How can this be achieved? Can someone help me out? g_energy on the .edr file (assuming that the vectors actually vary). Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] box vectors
Dear gmx_users, I am using gmx_4.0.7. I need to print the box vectors from the trajectory of a simulated system. How can this be achieved? Can someone help me out? Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_msd and pbc
Dear gmx_users, I was just wondering how the g_msd (of gmx 4.0.7) code, takes care of the PBC. e.g. If I want to calculate the lateral diffusion of a lipid bilayer and at some point of the trajectory, some lipid molecules, due to PBC in the lateral direction, might pop out from one side of the box and re-ener from the other side. I such a situation it should show a very lage msd, but actually in the g_msd code, this fact is taken care of. Can some one explain, how is this effect taken care of. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] box vectors
Thanks everyone for the responses. I should have framed my question much more precisely. I am trying to use the template.c code of (gmx_4.0.7) and within this, I want to take care of PBC. To do this, I should be having the knowledge of box dimensions. How can this done? I also know that the g_energy prints the box vector with the simulation time. But, trjconv -dump also writes the box vectors in the pdb file. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Dec 8, 2011 at 3:33 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 8/12/2011 4:36 AM, Chandan Choudhury wrote: Dear gmx_users, I am using gmx_4.0.7. I need to print the box vectors from the trajectory of a simulated system. How can this be achieved? Can someone help me out? g_energy on the .edr file (assuming that the vectors actually vary). Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] I want only coordinates in md.xtc/md.pdb
For any text file, use your favorite editor to delete all your water molecules. It will load very fast. For the xtc/trr files, use trjconv with an index file to write a new xtc/trr file without water molecules. Index file should contain the atom nos. of the molecules you want. trjconv -s a.tpr -f a.xtc/trr -n a.ndx -o b.xtc/trr chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Dec 8, 2011 at 10:56 AM, Saba Ferdous saba.bsbi...@iiu.edu.pkwrote: Dear Sir, I need to ask you that if I want only pdb coordinates in the resultant md-noPBC.xtc/md-noPBC.pdb file rather than the solvant atoms and coordinates then what should I do. because the water box causes very delay in loading of frames and its difficult to viualize the trajectory. kindly help me to get out of the broblem. I only want that my protein get display in vmd rather than the water box. the size of md-noPBC.xtc is 612 Mb md-noPBC.pdb is 13.2 GB analysis is getting very slow and system is hanging. kindly help me out to fix this problem. Regards Thanks -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] extend simulation without tpbconv
Hi gmx-users, Is it possible to extend a simulation with change in the output control parameter (nstxtcout)? I am aware of that tpbconv can extend a simulation with the same output controls as in the input tpr file. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] extending simulation with grompp incorporating velocities
Dear gmx users, A simulation was performed for 50 ns with ; RUN CONTROL integrator = md nsteps = 5000 dt = 0.001 ; OUTPUT CONTROL nstxout = 1000 nstvout = 1000 nstxtcout= 0 nstlog = 100 nstenergy= 100 The output produced were 0-50.edr, 0-50.trr, 0-50.log, 0-50.pdb state.cpt, state_prev.cpt. The simulation completed normally. After 50 ns, I intend to extend for 4 more ns, write the trajectory file frequently with ; RUN CONTROL integrator = md nsteps = 400 dt = 0.001 ; OUTPUT CONTROL nstxout = 00 nstvout = 00 nstxtcout= 10 nstlog = 500 nstenergy= 10 $grompp -f md.mdp -p topol.top -o md50-54.tpr -c 0-50.pdb -n index.ndx $gmxdump -s md50-54.tpr | more md50-54.tpr: inputrec: integrator = md nsteps = 400 init_step= 0 ns_type = Grid nstlist = 10 ndelta = 2 nstcomm = 1 comm_mode= Linear nstlog = 500 nstxout = 0 nstvout = 0 nstfout = 0 nstenergy= 10 nstxtcout= 10 init_t = 0 delta_t = 0.001 xtcprec = 1000 nkx = 22 nky = 22 nkz = 40 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 0 epsilon_surface = 0 optimize_fft = FALSE ePBC = xyz bPeriodicMols= FALSE bContinuation= FALSE bShakeSOR= FALSE etc = V-rescale epc = Berendsen epctype = Isotropic tau_p= 1 $mdrun_mpi-4.5.5 -s md50-54.tpr -c 50-54.pdb -x 50-54.xtc -e 50-54.edr -g 50-54.log -cpi state.cpt -nice 0 state.cpt is the output of the initial 50ns run. I have used state.cpt to incorporate the velocities frm the initial run. So, I would expect my 2nd simulation to get complete after running for 4 ns. But, that was not the case. I have checked the log file. The time clearly exceeds 4ns. $ tail -15 50-54.log DD step 54500989 load imb.: force 5.6% pme mesh/force 0.429 DD step 54500999 load imb.: force 6.0% pme mesh/force 0.428 Step Time Lambda 5450100054501.002590.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 1.82780e+023.37147e+028.77788e+011.92877e+013.90071e+01 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 5.96624e+027.91553e+04 -5.73437e+05 -2.73830e+04 -5.20402e+05 Kinetic En. Total EnergyTemperature Pressure (bar) 9.75908e+04 -4.22811e+052.97855e+02 -5.82198e+01 Kindly suggest what wrong am I doing. and how do I incorporate the velocity from my earlier run. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] extending simulation with grompp incorporating velocities
On Fri, Oct 21, 2011 at 10:26 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 21/10/2011 3:25 PM, Chandan Choudhury wrote: Dear gmx users, A simulation was performed for 50 ns with ; RUN CONTROL integrator = md nsteps = 5000 dt = 0.001 ; OUTPUT CONTROL nstxout = 1000 nstvout = 1000 nstxtcout= 0 nstlog = 100 nstenergy= 100 The output produced were 0-50.edr, 0-50.trr, 0-50.log, 0-50.pdb state.cpt, state_prev.cpt. The simulation completed normally. After 50 ns, I intend to extend for 4 more ns, write the trajectory file frequently with Use tpbconv -extend. See http://www.gromacs.org/**Documentation/How-tos/** Extending_Simulationshttp://www.gromacs.org/Documentation/How-tos/Extending_Simulations I was aware with the tpbconv command. But while using the tpbconv command, we cannot change the output frequency. If somehow the trajectory writing frequency can be changed, it will solve my curiosity. Chandan ; RUN CONTROL integrator = md nsteps = 400 dt = 0.001 ; OUTPUT CONTROL nstxout = 00 nstvout = 00 nstxtcout= 10 nstlog = 500 nstenergy= 10 $grompp -f md.mdp -p topol.top -o md50-54.tpr -c 0-50.pdb -n index.ndx $gmxdump -s md50-54.tpr | more md50-54.tpr: inputrec: integrator = md nsteps = 400 init_step= 0 ns_type = Grid nstlist = 10 ndelta = 2 nstcomm = 1 comm_mode= Linear nstlog = 500 nstxout = 0 nstvout = 0 nstfout = 0 nstenergy= 10 nstxtcout= 10 init_t = 0 delta_t = 0.001 xtcprec = 1000 nkx = 22 nky = 22 nkz = 40 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 0 epsilon_surface = 0 optimize_fft = FALSE ePBC = xyz bPeriodicMols= FALSE bContinuation= FALSE bShakeSOR= FALSE etc = V-rescale epc = Berendsen epctype = Isotropic tau_p= 1 $mdrun_mpi-4.5.5 -s md50-54.tpr -c 50-54.pdb -x 50-54.xtc -e 50-54.edr -g 50-54.log -cpi state.cpt -nice 0 state.cpt is the output of the initial 50ns run. I have used state.cpt to incorporate the velocities frm the initial run. So, I would expect my 2nd simulation to get complete after running for 4 ns. But, that was not the case. I have checked the log file. The time clearly exceeds 4ns. $ tail -15 50-54.log DD step 54500989 load imb.: force 5.6% pme mesh/force 0.429 DD step 54500999 load imb.: force 6.0% pme mesh/force 0.428 Step Time Lambda 5450100054501.002590.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 1.82780e+023.37147e+028.77788e+011.92877e+013.90071e+01 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 5.96624e+027.91553e+04 -5.73437e+05 -2.73830e+04 -5.20402e+05 Kinetic En. Total EnergyTemperature Pressure (bar) 9.75908e+04 -4.22811e+052.97855e+02 -5.82198e+01 Kindly suggest what wrong am I doing. and how do I incorporate the velocity from my earlier run. On the information given, I can't explain this observation. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] non-interactive script help
Thanks Terry. It worked. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Jul 22, 2011 at 12:00 PM, Terry terrence...@gmail.com wrote: You should issue a q command to save and quit. So choice.txt should look like: ri 1-20 ... ... ri 101-120 q Cheers. Terry On Fri, Jul 22, 2011 at 1:53 PM, Chandan Choudhury iitd...@gmail.com wrote: Hi gmx-users, I was trying to feed make_ndx with the non-interactive script, below is my command: The script called choice.txt contained: ri 1-20 ri 21-40 ri 41-60 ri 61-80 ri 81-100 ri 101-120 Initially, I used the bash shell, then csh and tcsh, but in both the cases it failed to produce the index_1.ndx file $make_ndx -f md20-80.tpr -o index_1.ndx choice.txt Found 162 atoms with resind.+1 in range 1-20 5 r_1-20 : 162 atoms Found 162 atoms with resind.+1 in range 21-40 6 r_21-40 : 162 atoms Found 162 atoms with resind.+1 in range 41-60 7 r_41-60 : 162 atoms Found 162 atoms with resind.+1 in range 61-80 8 r_61-80 : 162 atoms Found 162 atoms with resind.+1 in range 81-100 9 r_81-100 : 162 atoms Found 162 atoms with resind.+1 in range 101-120 10 r_101-120 : 162 atoms --- Program make_ndx, VERSION 4.5.4 Source code file: make_ndx.c, line: 965 Fatal error: Error reading user input For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Kindly help. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Residence time and trjorder
Carla, The g_residence.c is written in accord to gmx-4.5.4 format. What you can do is copy it to the src/tools directory. Make a subsequent changes in the Makefile present there and the do make to compile. This will generate g_residence executable, which can be used. But I did not understand, how the output trajectory of trjorder can be used for the analysis of the residence time of a water molecule i.e; the number of times a particular water molecule constantly stays in a radius of 5 A. Guidance is always welcome. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Jul 22, 2011 at 5:12 PM, Carla Jamous carlajam...@gmail.com wrote: Hi Baofu, Please can you tell me how to install g_residence.c in gromacs? If I understood well, the line command is the following: g_residence -s toplogy.tpr -f trajectory.xtc -o output What is the format of the output? Thank you, Carla On Tue, Jul 12, 2011 at 2:32 PM, Baofu Qiao qia...@gmail.com wrote: HI Carla, I wrote a similar code, see attached. But it is written for my condition. You should modify it accordingly. regards, Baofu Qiao On 07/12/2011 02:04 PM, Carla Jamous wrote: Dear gmx-users, I used trjorder in order to study the water molecules that are closer than 5 A from my protein. trjorder -s structure.tpr -f traj.xtc -n prot_water.ndx -o ordered.pdb -nshell nshell_.xvg -r 0.5 -b 0 -e 5000 But now I need to analyse the residence time of a water molecule, I mean the number of times a single water molecule stays in a radius of 5 A of the protein and divide this number by the total number of conformations, in order to have a pourcentage value. Please is there any gromacs tool able to do this calculation or else does anyone have an idea of how to do that? Thank you Carla -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] non-interactive script help
Hi gmx-users, I was trying to feed make_ndx with the non-interactive script, below is my command: The script called choice.txt contained: ri 1-20 ri 21-40 ri 41-60 ri 61-80 ri 81-100 ri 101-120 Initially, I used the bash shell, then csh and tcsh, but in both the cases it failed to produce the index_1.ndx file $make_ndx -f md20-80.tpr -o index_1.ndx choice.txt Found 162 atoms with resind.+1 in range 1-20 5 r_1-20 : 162 atoms Found 162 atoms with resind.+1 in range 21-40 6 r_21-40 : 162 atoms Found 162 atoms with resind.+1 in range 41-60 7 r_41-60 : 162 atoms Found 162 atoms with resind.+1 in range 61-80 8 r_61-80 : 162 atoms Found 162 atoms with resind.+1 in range 81-100 9 r_81-100: 162 atoms Found 162 atoms with resind.+1 in range 101-120 10 r_101-120 : 162 atoms --- Program make_ndx, VERSION 4.5.4 Source code file: make_ndx.c, line: 965 Fatal error: Error reading user input For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Kindly help. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Residence time and trjorder
Hi gmx-users, I tried installing the tool, g_residence.c I am using gromacs-4.0.7 I copied it to the src/tools. There, I executed make command # make g_residence cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -I/opt/fftw-3.2.2/include -L/opt/fftw-3.2.2/lib g_residence.c -o g_residence g_residence.c:42:22: fatal error: sysstuff.h: No such file or directory compilation terminated. make: *** [g_residence] Error 1 How do the tool can be installed? Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Jul 13, 2011 at 8:24 PM, XAvier Periole x.peri...@rug.nl wrote: Mark is right g_dist can help you for this but there is no specific tool calculating residence time ... I guess everyone dreams of someone writing it :)) On Jul 13, 2011, at 2:28 AM, Mark Abraham wrote: On 13/07/2011 5:52 PM, Carla Jamous wrote: Dear Xavier, my problem is the following: I'm trying to figure out if a water molecule is present in a specific area around my protein and if so, which water molecule is that and how long does it stay in that place. I think g_dist does this for a group containing a single water molecule. All you need to do write a script to iterate over each molecule, and then collate the statistics. Mark As you said, if I google residence time, here's the definition: *Residence time* (also known as *removal time*) is the average amount of time that a particle http://en.wikipedia.org/wiki/Particle spends in a particular system. But I don't find a tool to calculate this residence time in gromacs, so I'm trying to find a trick that can give me a pourcentage of the time of my simulation where a certain water molecule stays in the specific area of my protein. Regards, Carla On Tue, Jul 12, 2011 at 5:51 PM, XAvier Periole x.peri...@rug.nl wrote: Dear Boafu, This sounds like a great tool! Carla, note that once you've ordered the water molecules you loose the continuity of their trajectories ... that is because you order them in function of their distance to the protein. I am not sure the definition you give will give you the answer to the residence time. you can google residence time and proteins and see what come out :)) XAvier. On Jul 12, 2011, at 6:32 AM, Baofu Qiao wrote: HI Carla, I wrote a similar code, see attached. But it is written for my condition. You should modify it accordingly. regards, Baofu Qiao On 07/12/2011 02:04 PM, Carla Jamous wrote: Dear gmx-users, I used trjorder in order to study the water molecules that are closer than 5 A from my protein. trjorder -s structure.tpr -f traj.xtc -n prot_water.ndx -o ordered.pdb -nshell nshell_.xvg -r 0.5 -b 0 -e 5000 But now I need to analyse the residence time of a water molecule, I mean the number of times a single water molecule stays in a radius of 5 A of the protein and divide this number by the total number of conformations, in order to have a pourcentage value. Please is there any gromacs tool able to do this calculation or else does anyone have an idea of how to do that? Thank you Carla g_residence.c-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send
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 message already shows some hints. Try recompile FFTW with -fPIC. Jianguo __ From: Chandan Choudhury iitd...@gmail.com To: gmx-users gmx-users@gromacs.org Sent: Thursday, 2 June 2011 15:03:03 Subject: [gmx-users] gmx4.5.4 installation help Hello gmx-users, I am trying to install gmx-4.5.4 on a HPC Linux cluster x86_64. 1. I installed fftw 3.2.2 ./configure --prefix /soft/sudip/abc/execs/fftw/ --enable-single --enable-threads 2. Installing Gromacs : CPPFLAGS and LDFLAGS were written in bashrc file a) ./configure --prefix=/soft/sudip/abc/execs/gromacs/ execute successfully without any complain. b) make /usr/bin/ld: /soft/sudip/abc/execs/fftw/lib/libfftw3f.a(apiplan.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /soft/sudip/abc/execs/fftw/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src' make: *** [all-recursive] Error 1 shows problem. Couldnot understand the origin of problem. Kndly let me know if some information is missing. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Joshua L. Phillips Ph.D. Candidate - School of Engineering University of California, Merced jphilli...@ucmerced.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] gmx4.5.4 installation help
Hello gmx-users, I am trying to install gmx-4.5.4 on a HPC Linux cluster x86_64. 1. I installed fftw 3.2.2 ./configure --prefix /soft/sudip/abc/execs/fftw/ --enable-single --enable-threads 2. Installing Gromacs : CPPFLAGS and LDFLAGS were written in bashrc file a) ./configure --prefix=/soft/sudip/abc/execs/gromacs/ execute successfully without any complain. b) make /usr/bin/ld: /soft/sudip/abc/execs/fftw/lib/libfftw3f.a(apiplan.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /soft/sudip/abc/execs/fftw/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src' make: *** [all-recursive] Error 1 shows problem. Couldnot understand the origin of problem. Kndly let me know if some information is missing. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_hbond error
Hello gmx-users !! I tried using g_hbond tool to analyse h-bonds on my system. I could successfully execute the tool for two of my systems. But the third system should the memory problem. Below I have pasted my command and its output. *$ g_hbond -s ../md0-20.tpr -f 40-50.trr -n index_2.ndx -num hbnum.xvg -dist hbdist.xvg -ang hbang.xvg -life hblife.xvg -nice 0 -xvgr No option -sel Reading file ../md0-20.tpr, VERSION 4.0.7 (single precision) Specify 2 groups to analyze: Group 0 ( System) has 95687 elements Group 1 ( HNP) has10 elements Group 2 ( PE) has 192 elements Group 3 ( HP) has 216 elements Group 4 ( CPE) has 9 elements Group 5 ( SOL) has 95235 elements Group 6 ( Cl) has25 elements Group 7 ( N_H) has 126 elements Select a group: 5 Selected 5: 'SOL' Select a group: 7 Selected 7: 'N_H' Checking for overlap in atoms between SOL and N_H Calculating hydrogen bonds between SOL (95235 atoms) and N_H (126 atoms) Found 31795 donors and 31795 acceptors --- Program g_hbond, VERSION 4.0.7 Source code file: smalloc.c, line: 147 Fatal error: Not enough memory. Failed to calloc 31795 elements of size 4 for hb-hbmap[i] (called from file gmx_hbond.c, line 186) --- I Solve Problems (Pulp Fiction) : Cannot allocate memory Making hbmap structure...* Kindly help. -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: g_hbond error
I missed my Gromacs version. It's 4.0.7 -- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Apr 13, 2011 at 4:58 PM, Chandan Choudhury iitd...@gmail.comwrote: Hello gmx-users !! I tried using g_hbond tool to analyse h-bonds on my system. I could successfully execute the tool for two of my systems. But the third system should the memory problem. Below I have pasted my command and its output. *$ g_hbond -s ../md0-20.tpr -f 40-50.trr -n index_2.ndx -num hbnum.xvg -dist hbdist.xvg -ang hbang.xvg -life hblife.xvg -nice 0 -xvgr No option -sel Reading file ../md0-20.tpr, VERSION 4.0.7 (single precision) Specify 2 groups to analyze: Group 0 ( System) has 95687 elements Group 1 ( HNP) has10 elements Group 2 ( PE) has 192 elements Group 3 ( HP) has 216 elements Group 4 ( CPE) has 9 elements Group 5 ( SOL) has 95235 elements Group 6 ( Cl) has25 elements Group 7 ( N_H) has 126 elements Select a group: 5 Selected 5: 'SOL' Select a group: 7 Selected 7: 'N_H' Checking for overlap in atoms between SOL and N_H Calculating hydrogen bonds between SOL (95235 atoms) and N_H (126 atoms) Found 31795 donors and 31795 acceptors --- Program g_hbond, VERSION 4.0.7 Source code file: smalloc.c, line: 147 Fatal error: Not enough memory. Failed to calloc 31795 elements of size 4 for hb-hbmap[i] (called from file gmx_hbond.c, line 186) --- I Solve Problems (Pulp Fiction) : Cannot allocate memory Making hbmap structure...* Kindly help. -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_mindist clarification
Hi all !! Can some one clarify me what the g_mindist does. As far as I understood, it takes two inputs from the index file. If I have more than one entry in both of the indexes than how would g_mindist function? eg; echo 7 8 | g_mindist -s ../md30-60.tpr -n index.ndx -f ../30-60.part0004.trr -od mindist.xvg -nice 0 -b 35000 -e 4 -xvgr My 7th and 8th indexes are : [ N ] 1 11 20 29 38 47 56 65 74 83 92 101 110 119 128 137 146 155 164 173 183 193 202 211 220 229 238 247 256 265 274 283 292 301 310 319 328 337 346 355 365 375 384 393 402 411 420 429 438 447 456 465 474 483 492 501 510 519 528 537 547 557 566 575 584 593 602 611 620 629 638 647 656 665 674 683 692 701 710 719 729 739 748 757 766 775 784 793 802 811 820 829 838 847 856 865 874 883 892 901 911 921 930 939 948 957 966 975 984 993 1002 1011 1020 1029 1038 1047 1056 1065 1074 1083 1093 1103 1112 1121 1130 1139 1148 1157 1166 1175 1184 1193 1202 1211 1220 1229 1238 1247 1256 1265 1275 1285 1294 1303 1312 1321 1330 1339 1348 1357 1366 1375 1384 1393 1402 1411 1420 1429 1438 1447 1457 1467 1476 1485 1494 1503 1512 1521 1530 1539 1548 1557 1566 1575 1584 1593 1602 1611 1620 1629 1639 1649 1658 1667 1676 1685 1694 1703 1712 1721 1730 1739 1748 1757 1766 1775 1784 1793 1802 1811 [ O ] 1858 1960 2062 2164 2266 2368 2470 2572 2674 2776 2878 2980 3082 3184 3286 3388 3490 3592 3694 3796 3898 4000 4102 4204 4306 4408 4510 4612 4714 4816 4918 5020 5122 5224 5326 5428 5530 5632 5734 5836 5938 6040 6142 6244 6346 6448 6550 6652 6754 1865 1967 2069 2171 2273 2375 2477 2579 2681 2783 2885 2987 3089 3191 3293 3395 3497 3599 3701 3803 3905 4007 4109 4211 4313 4415 4517 4619 4721 4823 4925 5027 5129 5231 5333 5435 5537 5639 5741 5843 5945 6047 6149 6251 6353 6455 6557 6659 6761 1872 1974 2076 2178 2280 2382 2484 2586 2688 2790 2892 2994 3096 3198 3300 3402 3504 3606 3708 3810 3912 4014 4116 4218 4320 4422 4524 4626 4728 4830 4932 5034 5136 5238 5340 5442 5544 5646 5748 5850 5952 6054 6156 6258 6360 6462 6564 6768 1879 1981 2083 2185 2287 2389 2491 2593 2695 2797 2899 3001 3103 3205 3307 3409 3511 3613 3715 3817 3919 4021 4123 4225 4327 4429 4531 4633 4735 4837 4939 5041 5143 5245 5347 5449 5551 5653 5755 5857 5959 6061 6163 6265 6367 6469 6571 6673 6775 1886 1988 2090 2192 2294 2396 2498 2600 2702 2804 2906 3008 3110 3212 3314 3416 3518 3620 3722 3824 3926 4028 4130 4232 4334 4436 4538 4640 4742 4844 4946 5048 5150 5252 5354 5456 5558 5660 5762 5864 5966 6068 6170 6272 6374 6476 6578 6680 6782 1893 1995 2097 2199 2301 2403 2505 2607 2709 2811 2913 3015 3117 3219 3321 3423 3525 3627 3729 3831 3933 4035 4137 4239 4341 4443 4545 4647 4749 4851 4953 5055 5157 5259 5361 5463 5565 5667 5769 5871 5973 6075 6177 6279 6381 6483 6585 6687 6789 1900 2002 2104 2206 2308 2410 2512 2614 2716 2818 2920 3022 3124 3226 3328 3430 3532 3634 3736 3838 3940 4042 4144 4246 4348 4450 4552 4654 4756 4858 4960 5062 5164 5266 5368 5470 5572 5674 5776 5878 5980 6082 6184 6286 6388 6490 6592 6694 6796 1907 2009 2111 2213 2315 2417 2519 2621 2723 2825 2927 3029 3131 3233 3335 3437 3539 3641 3743 3845 3947 4049 4151 4253 4355 4457 4559 4661 4763 4865 4967 5069 5171 5273 5375 5477 5579 5681 5783 5885 5987 6089 6191 6293 6395 6497 6599 6701 6803 1914 2016 2118 2220 2322 2424 2526 2628 2730 2832 2934 3036 3138 3240 3342 3444 3546 3648 3750 3852 3954 4056 4158 4260 4362 4464 4566 4668 4770 4872 4974 5076 5178 5280 5382 5484 5586 5688 5790 5892 5994 6096 6198 6300 6402 6504 6606 6708 6810 1921 2023 2125 2227 2329 2431 2533 2635 2737 2839 2941 3043 3145 3247 3349 3451 3553 3655 3757 3859 3961 4063 4165 4267 4369 4471 4573 4675 4777 4879 4981 5083 5185 5287 5389 5491 5593 5695 5797 5899 6001 6103 6205 6307 6409 6511 6613 6715 6817 With one entry in the g_mindist (-od) and g_dist produces the same graph. -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fatal error (g_polystat)
Hello all !! I have a 30 ns trajectory in two parts (0-20 20-30). I am using Gromacs 4.0.7. I concatenated using trjcat (*echo 2 | trjconv -s md10-30.tpr -f 0-30.trr -o pbc_whole.trr -n index_grdf.ndx -nice 0*). Then I converted the concatenated trajectory into pbc trajectory using trjconv (*echo 2 | trjconv -f 0-30.trr -s md10-30.tpr -o pbc_whole.trr -n index_grdf.ndx -pbc whole*). The problem comes when I try to use the g_polystat utility (*echo 2 |* *g_polystat -s md10-30.tpr -f pbc_whole.trr -n index_grdf.ndx -o polystat_pbc.dat -xvgr*). The error message it produces is : *trn version: GMX_trn_file (single precision)* *Reading frame 0 time0.000 * *---* *Program g_dist, VERSION 4.0.7* *Source code file: mshift.c, line: 103* * * *Fatal error:* *Molecule in topology has atom numbers below and above natoms (162).* *You are probably trying to use a trajectory which does not match the first 162 atoms of the run input file.* *You can make a matching run input file with tpbconv.* --- The same error message erupts when I try to use g_dist. (echo 5 24 | g_dist -f pbc_whole.trr -s md10-30.tpr -n index_grdf.ndx -o dist_N-N.xvg). But when I execute g_mindist (echo 5 24 | g_mindist -f pbc_whole.trr -s md10-30.tpr -n index_grdf.ndx -o mindist_N-N.xvg). I works w/o any error message. Can figure out the probable cause. Please help. -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fatal error (g_polystat)
-- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Dec 24, 2010 at 3:13 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 24/12/2010 4:58 AM, Chandan Choudhury wrote: Hello all !! I have a 30 ns trajectory in two parts (0-20 20-30). I am using Gromacs 4.0.7. I concatenated using trjcat (*echo 2 | trjconv -s md10-30.tpr -f 0-30.trr -o pbc_whole.trr -n index_grdf.ndx -nice 0*). That looks like subset creation, not concatenation. Perhaps you should clarify what you think should be in all these files, and confirm with gmxcheck. Sorry. I wrongly copied the commands. The correct command was *trjcat -f 0-20.trr 20-30/20-30.trr -o analysis/0-30/0-30.trr -nice 0* *gmxcheck -f pbc_whole.trr *outputs Checking file pbc_whole.trr trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 162 Last frame 30 time 3.002 Item#frames Timestep (ps) Step310.1 Time310.1 Lambda 310.1 Coords 310.1 Velocities 310.1 Forces 0 Box 310.1 Then I converted the concatenated trajectory into pbc trajectory using trjconv (*echo 2 | trjconv -f 0-30.trr -s md10-30.tpr -o pbc_whole.trr -n index_grdf.ndx -pbc whole*). The problem comes when I try to use the g_polystat utility (*echo 2 |* *g_polystat -s md10-30.tpr -f pbc_whole.trr -n index_grdf.ndx -o polystat_pbc.dat -xvgr*). The error message it produces is : *trn version: GMX_trn_file (single precision)* *Reading frame 0 time0.000 * *---* *Program g_dist, VERSION 4.0.7* *Source code file: mshift.c, line: 103* * * *Fatal error:* *Molecule in topology has atom numbers below and above natoms (162).* *You are probably trying to use a trajectory which does not match the first 162 atoms of the run input file.* *You can make a matching run input file with tpbconv.* --- This means the contents of at least two of the .trr, .tpr and .ndx aren't describing the same thing. Mark The same error message erupts when I try to use g_dist. (echo 5 24 | g_dist -f pbc_whole.trr -s md10-30.tpr -n index_grdf.ndx -o dist_N-N.xvg). But when I execute g_mindist (echo 5 24 | g_mindist -f pbc_whole.trr -s md10-30.tpr -n index_grdf.ndx -o mindist_N-N.xvg). I works w/o any error message. Can figure out the probable cause. Please help. -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Reg: Putting molecules on one side of the box
Hi Vinoth !! Try genbox with increasing the vander Waal's radii. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Oct 4, 2010 at 5:03 PM, vinothkumar mohanakrishnan kmvin...@gmail.com wrote: hi Mark After deleting half the molecules of decane from the box and if i use genbox to add water then i will only get a mixture where as i want an interface to be formed.that will be more useful to me. Regards Vinoth On Mon, Oct 4, 2010 at 4:44 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Yes, giving you a set of commands would be the simplest thing for you :-) However I can't give you a set of commands for an arbitrary such operation, because there's a whole set of conditions you haven't stated. Moreover, figuring out the fine detail would take time that I don't have available. Finally, you wouldn't learn how to do solve such problems for yourself, and would remain dependent, instead of developing a set of skills that is useful for your work :-) Be sure to read the documentation for each of the tools I have mentioned, and please do ask a focussed question on the list if you run into problems. Good luck! Mark - Original Message - From: vinothkumar mohanakrishnan kmvin...@gmail.com Date: Monday, October 4, 2010 21:58 Subject: Re: [gmx-users] Reg: Putting molecules on one side of the box To: Discussion list for GROMACS users gmx-users@gromacs.org can you tell this with the help of the command that will be more useful Regards Vinoth On Fri, Sep 24, 2010 at 12:58 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Use genconf to replicate some suitable smaller box of decane to the full size, delete the second half of the decane molecules, then use genbox to fill the rest with water. Cunning use of genconf should allow you to select where the division lies. Mark - Original Message - From: vinothkumar mohanakrishnan kmvin...@gmail.com Date: Friday, September 24, 2010 17:22 Subject: [gmx-users] Reg: Putting molecules on one side of the box To: Discussion list for GROMACS users gmx-users@gromacs.org Hi all I have a triclinic box of length of 8*3*3 nm. i want to put water on one side of the box and say decane on the other side of the box. How to generate .gro for the water-decane mixture such that they form two distinct parts of the box. Regards Vinoth -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] editconf
-- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Aug 13, 2010 at 8:08 AM, Justin A. Lemkul jalem...@vt.edu wrote: abdullah ahmed wrote: Hello, I'd like to ask a question about the conversion of the results of minimization to pdb format. Here is what I do: 1. Apply pdb2gmx to the pdb file to convert it to .gro and .top (pdb2gmx -f -p -o) 2. Run editconf to define the box (editconf -d 1) 3. run gromp and mdrun for the minimization use mdrun -c . It will give you the required pdb file Chandan 4. Run editconf to re-convert back to pdb Unfortunately doing this seems to be adding some information into the pdb file that is not related to the atom coordinates. I think this might be trajectory data. Is there someway to remove this info? What is it exactly that you're seeing? The output .gro file from mdrun (which can be output as .pdb directly, if you prefer) contains only coordinates and box vectors, so anything else should just be comment lines. -Justin Thank you in advance, Abdullah -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] printing coordinates using template.c
Hello gmx users !! I was trying to use template.c. There I printed out the coordinates of a trajectory file using the printf statement as under: printf(Coordinates at t=%8.3f : %8.5f %8.5f %8.5f\n,fr.time,fr.x[n][XX],fr.x[n][YY],fr.x[n][ZZ]); The output was Reading frame 100 time 4400.000 Coordinates at t=4400.000 : 9.34053 4.26640 8.23887 This is the output of the 4400.000 th time or 100th frame of the first Atom in the trr file. Secondly, I dumped the 100th frame using tpbconv (of the same trajectory as above) as: trjconv -s *.tpr -f *.trr -dump 4400.00 -o frame100.pdb The frame100.pdb reads as: ATOM 1 N NGL A 1 93.405 42.664 82.389 1.00 0.00 ATOM 2 H1 NGL A 1 93.849 42.216 81.599 1.00 0.00 ATOM 3 H2 NGL A 1 93.914 43.464 82.737 1.00 0.00 ATOM 4 H3 NGL A 1 93.577 41.958 83.090 1.00 0.00 ATOM 5 CA NGL A 1 91.980 42.980 82.205 1.00 0.00 ATOM 6 HA NGL A 1 91.538 41.996 82.050 1.00 0.00 ATOM 7 CB NGL A 1 91.260 43.708 83.336 1.00 0.00 ATOM 8 HB1 NGL A 1 90.206 43.782 83.068 1.00 0.00 ATOM 9 HB2 NGL A 1 91.603 44.742 83.372 1.00 0.00 We can clearly see the difference in the coordinates of the 1st Atom (ATOM 1 N). That is the coordinates produced by the template are different than those of trjconv's. Can someone help me out to correctly printf the x, y z coordinate using the template.c file. Thanks Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] template.c
The suggestions were very helpful. Thanks Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Sun, May 30, 2010 at 11:32 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Chandan, The problem is that with floating points the equality in if (fr.time == (4000.000 + (50.0 * inc))) is very unlikely to be satisfied at any time. To compare floating point numbers, you'll have to check whether the value is within a certain interval. But Jussi's approach is far more convenient in this particular case. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] template.c
Hello all !!
I was playing around with template.c and stuck in a problem.
In the program inside the do loop i.e;
/* This is the main loop over frames */
do {
/* coordinates are available in the vector fr.x
* you can find this and all other structures in
* the types directory under the gromacs include dir.
* Note how flags determines wheter to read x/v/f!
*/
printf (%8.3f\n, fr.time);
if (fr.time == (4000.000 + (50.0 * inc)))
printf (test);
{
for (ra=0; rai;ra++)
{
}
} inc ++;
}while (read_next_frame(status,fr));
The 1st printf statement do prints the frame time. While the 2nd printf
inside the if loop doesnt print any thing, meaning that the if condition is
not being satisfied. I want to execute the statements under if loop after
each 50 ps time.
Can some point out what wrong am I doing.
Thanks
--
Chandan kumar Choudhury
NCL, Pune
INDIA
--
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Re: [gmx-users] gromacs doubt
Have a loolk at http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings Chadnan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, May 13, 2010 at 10:34 AM, manjula kasinathan manju...@gmail.comwrote: Hi all i have done protein protein interaction and the complex structure was taken for MD simulation using Gromacs. the length of the protein was around 1100 aa. while performing mdrun step for position restrain i got error. i have carried out mdrun for 1ps and the command given for mdrun and position restrain are grompp -f *.pdb -c *.gro -p top.top -o *.tpr mdrun -v -deffnm pr error i got was starting mdrun '? in water' 500 steps, 1.0 ps. step 400, remaining runtime: 133 s Step 416, time 0.832 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000577, max 0.008379 (between atoms 5530 and 5532) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 8190 8191 30.70.1014 0.1000 0.1000 Step 419, time 0.838 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000874, max 0.019432 (between atoms 5526 and 5527) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 112113 31.00.1017 0.1002 0.1000 Step 430, time 0.86 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 158552932798158.562500, max 14888250728513536.00 (between atoms 1734 and 1735) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 4469 4471 66.70.1327 0.5535 0.1330 4469 4470 69.60.1227 0.5336 0.1230 8001 8003 47.00.0999 0.0998 0.1000 7995 7996 30.00.1001 0.0999 0.1000 7970 7971 34.00.0999 0.1002 0.1000 t = 0.860 ps: Water molecule starting at atom 81142 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates could any one pls help me to overcome this problem.how give me some ideas. looking forward for a solution. thanx in advance. -- With Regards, Manjulakasinathan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Understanding template.c
Hi gmx users !! I want to read the trajectory file (*.trr ), produced as a result of mdrun. I came to know that a file template.c already exists to facilate my process. I could compile and execute the template.c. Like printf(Atom name: %s\n,*(top.atoms.atomname[n])); printf(Atom charge: %f\n,top.atoms.atom[n].q); produces the Atom Name and the corresponding partial charges. respectively. I could also print the x, y, z coordinate for each frame present in the trr file. What am I looking for is, how can I print the Atom number, Residue name, residue number? I was unable to find it in the program template.c. I would also like to know how do you prompt -s / -f / -n etc. option during executing gmx commands? Thanks for your cooperation. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Amino acid simulation
Thanks Justin. It worked perfectly. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Apr 13, 2010 at 1:08 AM, Justin A. Lemkul jalem...@vt.edu wrote: Chandan Choudhury wrote: Hello gmx-users I am trying to simulate an amino acid (say GLN). It can be as a zwitterionic form or uncharged ends. Neither ffamber or ffopls force fields has a complete parameter for them. While in ffamber, I have the This is not true. OPLS can handle isolated amino acids, you just have to manually choose the termini in pdb2gmx (using -ter). Use the zwitterion forms of the termini, since in fact, you have a zwitterion. -Justin parameters for CGLU and NGLU, but not for a Glutamine. Do I need to define it there, or there is some way out. If I need to define it, how do I retrive the partial charges. Any insight would be very helpful. Thanks Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Amino acid simulation
Hello gmx-users I am trying to simulate an amino acid (say GLN). It can be as a zwitterionic form or uncharged ends. Neither ffamber or ffopls force fields has a complete parameter for them. While in ffamber, I have the parameters for CGLU and NGLU, but not for a Glutamine. Do I need to define it there, or there is some way out. If I need to define it, how do I retrive the partial charges. Any insight would be very helpful. Thanks Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] restarting mdrun
Hello gmxusers !!! I want to continue my simulation, from where the point where it stopped. The gmxcheck on .trr and cpt files are as: $gmxcheck -f state.cpt Checking file state.cpt # Atoms 186864 Last frame -1 time 9362.500 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 $gmxcheck -f 5-10.trr Checking file 5-10.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 5169.500 # Atoms 186864 Reading frame8000 time 9169.500 Item#frames Timestep (ps) Step 83950.5 Time 83950.5 Lambda83950.5 Coords83950.5 Velocities83950.5 Forces 0 Box 83950.5 There is a mismatch of time in both the outputs. The date of modification of both the files as shown are: Feb 15 19:55 state.cpt $date -r 5-10.trr Mon Feb 15 19:59:56 IST 2010 The cpt file shows time greater than the trr file. But the time of modification of cpt file is less than trr file. Cannot understand the, how to restart the mdrun. And the size of the trr file is 36GB. Can I use the append flag in mdrun for gmx 4.0.5. Kindly suggest. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] restarting mdrun
Hi Mark !!! Thanks for answering. My query is how do I restart my mdrun because the command nohup mpirun -np 16 -machinefile mac mdrun -s md5-10.tpr -cpi state.cpt -append will not start from where the trajectory was stopped (i.e; time 9169.500). As this command will continue the simulation from where the cpt file was written. Any suggestions?? chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Feb 16, 2010 at 9:36 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 17/02/10 02:52, Chandan Choudhury wrote: Hello gmxusers !!! I want to continue my simulation, from where the point where it stopped. The gmxcheck on .trr and cpt files are as: $gmxcheck -f state.cpt Checking file state.cpt # Atoms 186864 Last frame -1 time 9362.500 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 $gmxcheck -f 5-10.trr Checking file 5-10.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 5169.500 # Atoms 186864 Reading frame8000 time 9169.500 Item#frames Timestep (ps) Step 83950.5 Time 83950.5 Lambda83950.5 Coords83950.5 Velocities83950.5 Forces 0 Box 83950.5 There is a mismatch of time in both the outputs. The date of modification of both the files as shown are: Feb 15 19:55 state.cpt $date -r 5-10.trr Mon Feb 15 19:59:56 IST 2010 The cpt file shows time greater than the trr file. But the time of modification of cpt file is less than trr file. If the simulation stopped catastrophically, then the timestamp could easily differ, especially if the .cpt is opened, written to and closed periodically, and the .trr is open continuously. Cannot understand the, how to restart the mdrun. And the size of the trr file is 36GB. Can I use the append flag in mdrun for gmx 4.0.5. Search the webpage for suggestions. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] restarting mdrun
Thanks Justin !! But my state_prev.cpt file shows $gmxcheck -f state_prev.cpt Checking file state_prev.cpt # Atoms 186864 Last frame -1 time 9346.700 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 Here also the time is greater than the .trr file. Cant understand how to overcome it. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Feb 16, 2010 at 11:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: Chandan Choudhury wrote: Hi Mark !!! Thanks for answering. My query is how do I restart my mdrun because the command nohup mpirun -np 16 -machinefile mac mdrun -s md5-10.tpr -cpi state.cpt -append will not start from where the trajectory was stopped (i.e; time 9169.500). As this command will continue the simulation from where the cpt file was written. Right, it will start from whenever the checkpoint was written. You should also have a state_prev.cpt that is a backup in case this type of thing happens; it may help. Regardless, with a 36-GB .trr file, the -append option will not work. Leave it out and use trjcat later. -Justin Any suggestions?? chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Feb 16, 2010 at 9:36 PM, Mark Abraham mark.abra...@anu.edu.aumailto: mark.abra...@anu.edu.au wrote: On 17/02/10 02:52, Chandan Choudhury wrote: Hello gmxusers !!! I want to continue my simulation, from where the point where it stopped. The gmxcheck on .trr and cpt files are as: $gmxcheck -f state.cpt Checking file state.cpt # Atoms 186864 Last frame -1 time 9362.500 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 $gmxcheck -f 5-10.trr Checking file 5-10.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 5169.500 # Atoms 186864 Reading frame8000 time 9169.500 Item#frames Timestep (ps) Step 83950.5 Time 83950.5 Lambda83950.5 Coords83950.5 Velocities83950.5 Forces 0 Box 83950.5 There is a mismatch of time in both the outputs. The date of modification of both the files as shown are: Feb 15 19:55 state.cpt $date -r 5-10.trr Mon Feb 15 19:59:56 IST 2010 The cpt file shows time greater than the trr file. But the time of modification of cpt file is less than trr file. If the simulation stopped catastrophically, then the timestamp could easily differ, especially if the .cpt is opened, written to and closed periodically, and the .trr is open continuously. Cannot understand the, how to restart the mdrun. And the size of the trr file is 36GB. Can I use the append flag in mdrun for gmx 4.0.5. Search the webpage for suggestions. Mark --gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] restarting mdrun
Below is my .mdp file. The timestep dt shows as 0.001 ps title= protein cpp = /lib/cpp ; RUN CONTROL integrator = md nsteps = 300 dt = 0.001 ; NEIGHBOR SEARCHING nstlist = 10 ns_type = grid pbc = xyz rlist= 0.9 ; OUTPUT CONTROL nstxout = 500 nstvout = 500 nstxtcout= 0 nstlog = 10 constraints = all-bonds nstenergy= 100 ; OPTION FOR ELECTROSTATIC AND VDW coulombtype = PME rcoulomb_switch = 0 rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon_r= 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw_switch = 0 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = 2.5 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.28 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS tcoupl = V-rescale tc_grps = SOL Protein Na tau_t= 0.1 0.1 0.1 ref_t= 300 300 300 Pcoupl = Berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = yes gen_temp = 300 -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Feb 16, 2010 at 11:27 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 17/02/10 04:43, Chandan Choudhury wrote: Thanks Justin !! But my state_prev.cpt file shows $gmxcheck -f state_prev.cpt Checking file state_prev.cpt # Atoms 186864 Last frame -1 time 9346.700 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 Here also the time is greater than the .trr file. Cant understand how to overcome it. Your checkpoint interval need not match your .trr-writing interval - see your .mdp file. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Restarting mdrun
Thanks Lum !!! I had already used the suggestion you mentioned. But my problem is somewhat different. You can go through my previous mail, for more information. Thanks. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Feb 16, 2010 at 11:42 PM, Lum Nforbi lumngwe...@gmail.com wrote: Hi Chadan, I have used the two commands below to CONTINUE a run and they worked fine for me. I am also using gromacs-4.0.5. tpbconv -s wfullmdrun_extend2.tpr -extend 2000 -o wfullmdrun_extend3.tpr mdrun -s wfullmdrun_extend3.tpr -o wfullmdrun_traj.trr -e wfullmdrun_ener.edr -g md.log -cpi state_prev.cpt -append The first command includes the amount of time by which you want to extend your run. The second one just appends the results to your existing files. In this second command, you are using the new .tpr file you created in the first command. Use the state.cpt file instead of the state_prev.cpt file in order to avoid losing time. Hope this helps. Lum On 17/02/10 02:52, Chandan Choudhury wrote: Hello gmxusers !!! I want to continue my simulation, from where the point where it stopped. The gmxcheck on .trr and cpt files are as: $gmxcheck -f state.cpt Checking file state.cpt # Atoms 186864 Last frame -1 time 9362.500 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 $gmxcheck -f 5-10.trr Checking file 5-10.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 5169.500 # Atoms 186864 Reading frame8000 time 9169.500 Item#frames Timestep (ps) Step 83950.5 Time 83950.5 Lambda83950.5 Coords83950.5 Velocities83950.5 Forces 0 Box 83950.5 There is a mismatch of time in both the outputs. The date of modification of both the files as shown are: Feb 15 19:55 state.cpt $date -r 5-10.trr Mon Feb 15 19:59:56 IST 2010 The cpt file shows time greater than the trr file. But the time of modification of cpt file is less than trr file. If the simulation stopped catastrophically, then the timestamp could easily differ, especially if the .cpt is opened, written to and closed periodically, and the .trr is open continuously. Cannot understand the, how to restart the mdrun. And the size of the trr file is 36GB. Can I use the append flag in mdrun for gmx 4.0.5. Search the webpage for suggestions. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem installin gmx
Thanks Mark. What I did I copied gmx from one of the servers, in which it was installed paralley. Will have a look at your suggestions, if I get into trouble. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Sat, Feb 13, 2010 at 10:31 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 13/02/10 15:29, Chandan Choudhury wrote: What is a cross-compiler? One that compiles an executable for architecture other than the one on which compilation occurs. My system is x86_64 x86_64 x86_64 GNU/Linux model name: Intel(R) Xeon(R) CPU E5520 @ 2.27GHz vendor id: GenuineIntel OK, well that shouldn't be problematic. My next guess is that your mpicc will only compile executables that will run with mpirun - this is a special case of cross-compilation. During the build process, GROMACS builds the C program mknb on the compilation machine, and then executes it normally on the compilation machine generate source files, which are then compiled for the execution machine. However if the MPI compiler can only generate code suitable for execution in the parallel environment, this procedure will fail. In my experience, that's abnormal behaviour for mpicc - perhaps this suggests an update of the MPI library. You can see if this is the problem by seeing whether you get the same issue with ./configure --disable-mpi from a fresh copy of the GROMACS source. If this works correctly, then you can work around the issue by running ./configure --enable-mpi on a different fresh copy of the source, then copying over the contents of src/gmxlib/nonbonded/nb_kernel from the MPI-disabled version to the MPI-enabled version (perhaps then running touch src/gmxlib/nonbonded/nb_kernel/kernel-stamp) to make sure the Makefiles are fooled). Now when you issue make, at the relevant point the make process will avoid needing to run mknb. Another solution is to run ./configure --enable-mpi, then edit src/gmxlib/nonbonded/nb_kernel/Makefile to correctly run mknb as a parallel program, boot a parallel environment, then run make. Mark Chandan kumar Choudhury NCL, Pune INDIA On Sat, Feb 13, 2010 at 6:30 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 02/13/10, *Chandan Choudhury * iitd...@gmail.com mailto:iitd...@gmail.com wrote: Hello gmx users !! I installed successfully installed fftw. Then tried compiling gmx parallely I executed the command $ ./configure --enable-mpi --prefix=/home/vanka/NUM-GEN/GRO/ It didnot show any problem. $make make[5]: Entering directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib/nonbonded/nb_kernel' rm -f kernel-stamp ./mknb -software_invsqrt make[5]: *** [kernel-stamp] Segmentation fault make[5]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib/nonbonded/nb_kernel' make[4]: *** [all-recursive] Error 1 make[4]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib/nonbonded' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src' make: *** [all-recursive] Error 1 This usually means you're using a system that needs a cross-compiler, but since you haven't told us anything about your computer system, you're making everybody's life hard :-) Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem installin gmx
Hello gmx users !! I installed successfully installed fftw. Then tried compiling gmx parallely I executed the command $ ./configure --enable-mpi --prefix=/home/vanka/NUM-GEN/GRO/ It didnot show any problem. $make make[5]: Entering directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib/nonbonded/nb_kernel' rm -f kernel-stamp ./mknb -software_invsqrt make[5]: *** [kernel-stamp] Segmentation fault make[5]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib/nonbonded/nb_kernel' make[4]: *** [all-recursive] Error 1 make[4]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib/nonbonded' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src' make: *** [all-recursive] Error 1 Cannot get the error Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem installin gmx
What is a cross-compiler? My system is x86_64 x86_64 x86_64 GNU/Linux model name: Intel(R) Xeon(R) CPU E5520 @ 2.27GHz vendor id: GenuineIntel Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Sat, Feb 13, 2010 at 6:30 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 02/13/10, *Chandan Choudhury * iitd...@gmail.com wrote: Hello gmx users !! I installed successfully installed fftw. Then tried compiling gmx parallely I executed the command $ ./configure --enable-mpi --prefix=/home/vanka/NUM-GEN/GRO/ It didnot show any problem. $make make[5]: Entering directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib/nonbonded/nb_kernel' rm -f kernel-stamp ./mknb -software_invsqrt make[5]: *** [kernel-stamp] Segmentation fault make[5]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib/nonbonded/nb_kernel' make[4]: *** [all-recursive] Error 1 make[4]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib/nonbonded' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src' make: *** [all-recursive] Error 1 This usually means you're using a system that needs a cross-compiler, but since you haven't told us anything about your computer system, you're making everybody's life hard :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Software inconsistency error: Not enough water
Thanks berk. By the way, if I dont give -p topol.top as input to genion, then genion executes. In this case, I manually edit the topology file and add the ion information. [ molecules ] ; Compound#mols Protein_A 1 Protein_B 1 Protein_C 1 Protein_D 1 Protein_E 1 SOL32 SOL46 SOL 3 SOL13 SOL 19791 Na 48 This is my part of topology after adding ions (Na). In the previous case of genion was only considering first SOL information, which has only 32 molecules. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Feb 11, 2010 at 3:38 PM, Berk Hess g...@hotmail.com wrote: Hi, This error message in incorrect, it is probably not a software inconsistency. Looking at the code, it seems the problem is that the topology file you provided does not have enough SOL molecules in the [molecules ] section. I'll fix this error message for the next release. Berk -- From: iitd...@gmail.com Date: Thu, 11 Feb 2010 12:48:53 +0530 To: gmx-users@gromacs.org Subject: [gmx-users] Software inconsistency error: Not enough water Hello gmxusers !! I am simulating a protein and it is bound to ATP. Simulation of protein alone (without) works fine. Solely ATP simulation too works. But the problem arises on adding ions to the protein + ATP (1QHH.pdb) file. Error: $ genion -s em.tpr -o ion.pdb -p topol.top -np 48 WARNING: turning of free energy, will use lambda=0 Reading file em.tpr, VERSION 4.0.7 (single precision) Using a coulomb cut-off of 0.9 nm Will try to add 48 Na ions and 0 Cl ions. Select a continuous group of solvent molecules Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Group 0 ( System) has 70056 elements Group 1 ( Protein) has 10214 elements Group 2 ( Protein-H) has 5107 elements Group 3 ( C-alpha) has 623 elements Group 4 (Backbone) has 1869 elements Group 5 ( MainChain) has 2488 elements Group 6 (MainChain+Cb) has 3083 elements Group 7 ( MainChain+H) has 3099 elements Group 8 ( SideChain) has 7115 elements Group 9 ( SideChain-H) has 2619 elements Group10 ( Prot-Masses) has 10214 elements Group11 ( Non-Protein) has 59842 elements Group12 ( ATP) has43 elements Group13 ( SOL) has 59799 elements Group14 ( Other) has 59842 elements Select a group: 13 Selected 13: 'SOL' Number of (3-atomic) solvent molecules: 19933 Processing topology Back Off! I just backed up temp.top to ./#temp.top.1# --- Program genion, VERSION 4.0.7 Source code file: gmx_genion.c, line: 269 Software inconsistency error: Not enough water --- Though my system has sufficient amount of water (19933) molecules. Can not understand the error. Any information would be useful. Chadan -- Chandan kumar Choudhury NCL, Pune INDIA -- Express yourself instantly with MSN Messenger! MSN Messengerhttp://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Software inconsistency error: Not enough water
Hello gmxusers !! I am simulating a protein and it is bound to ATP. Simulation of protein alone (without) works fine. Solely ATP simulation too works. But the problem arises on adding ions to the protein + ATP (1QHH.pdb) file. Error: $ genion -s em.tpr -o ion.pdb -p topol.top -np 48 WARNING: turning of free energy, will use lambda=0 Reading file em.tpr, VERSION 4.0.7 (single precision) Using a coulomb cut-off of 0.9 nm Will try to add 48 Na ions and 0 Cl ions. Select a continuous group of solvent molecules Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Group 0 ( System) has 70056 elements Group 1 ( Protein) has 10214 elements Group 2 ( Protein-H) has 5107 elements Group 3 ( C-alpha) has 623 elements Group 4 (Backbone) has 1869 elements Group 5 ( MainChain) has 2488 elements Group 6 (MainChain+Cb) has 3083 elements Group 7 ( MainChain+H) has 3099 elements Group 8 ( SideChain) has 7115 elements Group 9 ( SideChain-H) has 2619 elements Group10 ( Prot-Masses) has 10214 elements Group11 ( Non-Protein) has 59842 elements Group12 ( ATP) has43 elements Group13 ( SOL) has 59799 elements Group14 ( Other) has 59842 elements Select a group: 13 Selected 13: 'SOL' Number of (3-atomic) solvent molecules: 19933 Processing topology Back Off! I just backed up temp.top to ./#temp.top.1# --- Program genion, VERSION 4.0.7 Source code file: gmx_genion.c, line: 269 Software inconsistency error: Not enough water --- Though my system has sufficient amount of water (19933) molecules. Can not understand the error. Any information would be useful. Chadan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun append problem
Dear Justin Thanks for your reply. I didnot get any fatal error. Since, the mdrun has started (mdrun -s spc_25_eq.tpr -cpi state.cpi -c spc_25_eq.pdb -o spc_25_eq.trr -e spc_25_eq.edr -g spc_25_eq.log -append yes ), it has created new state.cpi. So I now I cannot verify it. From now, I will definetly check the .trr and .cpi before issuing the append command. And I thing, does the value of - append i.e 'yes' is compulsion for appending or just -append would work? I am asking this because once I restartd mdrun as -cpi state.cpi -append, with no 'yes' value to mdrun. It then created new gro, trr and edr files. What I found here was the .trr (generated using cpi flag) file had all the frames. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Feb 8, 2010 at 5:21 PM, Justin A. Lemkul jalem...@vt.edu wrote: Chandan Choudhury wrote: Hello gmxusers !! gmxcheck on #spc_25_eq.trr prints: (#spc_25_eq.trr is the renamed from #spc_25_eq.trr.1#. mdrun was stopped due to insufficient space) Checking file #spc_25_eq.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 2000.000 # Atoms 33885 Reading frame 200 time 3000.000 WARNING: Incomplete frame: nr 214 time 3070 Item#frames Timestep (ps) Step 2145 Time 2145 Lambda 2145 Coords 2145 Velocities 2145 Forces 0 Box2145 on restarting the mdrun from state.cpi mdrun -s spc_25_eq.tpr -cpi state.cpi -c spc_25_eq.pdb -o spc_25_eq.trr -e spc_25_eq.edr -g spc_25_eq.log -append yes gmxcheck on spc_25_eq.trr prints: Checking file spc_25_eq.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 2000.000 # Atoms 33885 Last frame 13 time 2065.000 Item#frames Timestep (ps) Step144.9 Time144.9 Lambda 144.9 Coords 144.9 Velocities 144.9 Forces 0 Box 144.9 It seems that the -append command didn't append. How can the appending be done. What time does state.cpi correspond to? You can use gmxcheck for that. If you're taking up from the original time point, then you won't get continuation. Further, above, you checked #spc_25_eq.trr no spc_25_eq.trr - are you sure you've got all your file names correct? The combination of -cpi -append should work quite well, although I think there are still some issues with file sizes 2GB, but that does not appear to be the case here (you would've gotten a fatal error). -Justin Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ATP for
Hi Tom!! Thanks for the information. I went through the paper and added the new O3 atom type. One unusual thing I noticed was that the sum of the partial charges on the atoms of AT P at the last column of http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/ATP.prepfile is -12.7145. How come fractional? and the hydrogens of phosphate are missing. How can it be overcome? Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Sat, Feb 6, 2010 at 1:13 AM, TJ Piggot t.pig...@bristol.ac.uk wrote: From the Carlson et al. paper where these ATP parameters were published and through choosing the appropriate amber_X atom types from the .atp (and the corresponding values for these types in the nb and bon .itp files). As I mentioned previously you need to add a new O3 atom type to these files based on the information in the Carlson paper. If you have a look at one of the entries from the ffamberXX.rtp file and work out how this is used by pdb2gmx it should become clear what you need to do to add the ATP to the forcefield. Cheers Tom --On Saturday, February 06, 2010 00:05:10 +0530 Chandan Choudhury iitd...@gmail.com wrote: Hi Thomas ! Creating a new entry in the .rtp, nb.itp needs charge, radius, epsilon values etc. values. Where to get these values Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Feb 5, 2010 at 6:54 PM, Thomas Piggot t.pig...@bristol.ac.uk wrote: Not sure about amb2gmx.pl or acpypi but you can do this by hand. Consult the GROMACS manual (Chapter 4) for the equations to convert the parameters into GROMACS format. I would also say that the easiest way would be to create a new entry in the .rtp and then also add the appropriate bonded parameters into the bon.itp file, making sure to include the bonded parameters for the new O3 atom type. Do note that you need to also add this new atom type for the O3 oxygen into the .atp file and the non-bonded parameters for the atom type into the nb.itp file. You can also add entries into the .hdb to allow pdb2gmx to add the appropriate hydrogens to your ATP if so desired. If not, your input pdb for pdb2gmx will need to have these hydrogens already included. Cheers Tom Chandan Choudhury wrote: Hello gmx users, I need to use ATP's parameter for amber port in gromacs. The atp.prep and frcmod.phos for ATP can be found at http://www.pharmacy.manchester.ac.uk/bryce/ahttp://www.pharmacy.manchester.ac.uk/bryce/amber *mdrun -s spc_25_eq.tpr -cpi state.cpi -c spc_25_eq.pdb -o spc_25_eq.trr -e spc_25_eq.edr -g spc_25_eq.log -append yes* mber http://www.pharmacy.manchester.ac.uk/bryce/amber. How can I use it in ffamber. The program amb2gmx.pl http://amb2gmx.pl needs amber to be installed, which is not present. Same with ACPYPI. Any suggestion will be very helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- Thomas Piggot University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] compilation problems orte error
As Justin said give the command line options for mdrun and also check that your mpi environment is running. Better to run a parallel job and check its output. Chadnan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Feb 8, 2010 at 8:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jennifer Williams wrote: Dear All, I am having problems compiling gromacs 4.0.7 in parallel. I am following the Quick and Dirty Installation instructions on the gromacs webpage. I downloaded the the versions of fftw, OpenMPI and gromacs-4.0.7 following these instructions. Everything seems to compile OK and I get all the serial executables including mdrun written to my bin directory and they seem to run fine. However when I try to run mdrun_mpi on 6 nodes I get the following: [vlxbig16:08666] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 [vlxbig16:08667] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 [vlxbig16:08700] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 [vlxbig16:08670] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 [vlxbig16:08681] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 [vlxbig16:08659] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 -- It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): orte_rml_base_select failed -- Returned value -13 instead of ORTE_SUCCESS Does anyone have any idea what is causing this? Computer support at my University is not sure. How are you launching mdrun_mpi (command line)? -Justin Thanks -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ATP for
Thanks Tom. Some how only the negative charges were being added in spreadsheet. So, I got charge around -12. I am simulating 1QHH. It has ATP in it, the structure of the ligand in the rcsb (http://www.pdb.org/pdb/explore/explore.do?structureId=1QHH) shows ATP with hydrogen. -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Feb 8, 2010 at 8:34 PM, Thomas Piggot t.pig...@bristol.ac.ukwrote: Are you sure you added it up correctly? I get a number very close to -4. There is no hydrogen on the gamma phosphate as it was parameterised in this way. If the environment in which your ATP is located suggests that the gamma phosphate should be protonated then you need to use other ATP parameters which include this hydrogen (such as those in the GROMOS forcefield). Cheers Tom Chandan Choudhury wrote: Hi Tom!! Thanks for the information. I went through the paper and added the new O3 atom type. One unusual thing I noticed was that the sum of the partial charges on the atoms of AT P at the last column of http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/ATP.prepfile is -12.7145. How come fractional? and the hydrogens of phosphate are missing. How can it be overcome? Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Sat, Feb 6, 2010 at 1:13 AM, TJ Piggot t.pig...@bristol.ac.ukmailto: t.pig...@bristol.ac.uk wrote: From the Carlson et al. paper where these ATP parameters were published and through choosing the appropriate amber_X atom types from the .atp (and the corresponding values for these types in the nb and bon .itp files). As I mentioned previously you need to add a new O3 atom type to these files based on the information in the Carlson paper. If you have a look at one of the entries from the ffamberXX.rtp file and work out how this is used by pdb2gmx it should become clear what you need to do to add the ATP to the forcefield. Cheers Tom --On Saturday, February 06, 2010 00:05:10 +0530 Chandan Choudhury iitd...@gmail.com mailto:iitd...@gmail.com wrote: Hi Thomas ! Creating a new entry in the .rtp, nb.itp needs charge, radius, epsilon values etc. values. Where to get these values Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Feb 5, 2010 at 6:54 PM, Thomas Piggot t.pig...@bristol.ac.uk mailto:t.pig...@bristol.ac.uk wrote: Not sure about amb2gmx.pl http://amb2gmx.pl or acpypi but you can do this by hand. Consult the GROMACS manual (Chapter 4) for the equations to convert the parameters into GROMACS format. I would also say that the easiest way would be to create a new entry in the .rtp and then also add the appropriate bonded parameters into the bon.itp file, making sure to include the bonded parameters for the new O3 atom type. Do note that you need to also add this new atom type for the O3 oxygen into the .atp file and the non-bonded parameters for the atom type into the nb.itp file. You can also add entries into the .hdb to allow pdb2gmx to add the appropriate hydrogens to your ATP if so desired. If not, your input pdb for pdb2gmx will need to have these hydrogens already included. Cheers Tom Chandan Choudhury wrote: Hello gmx users, I need to use ATP's parameter for amber port in gromacs. The atp.prep and frcmod.phos for ATP can be found at http://www.pharmacy.manchester.ac.uk/bryce/a http://www.pharmacy.manchester.ac.uk/bryce/amber _mdrun -s spc_25_eq.tpr -cpi state.cpi -c spc_25_eq.pdb -o spc_25_eq.trr -e spc_25_eq.edr -g spc_25_eq.log -append yes_ mber http://www.pharmacy.manchester.ac.uk/bryce/amber. How can I use it in ffamber. The program amb2gmx.pl http://amb2gmx.pl http://amb2gmx.pl needs amber to be installed, which is not present. Same with ACPYPI. Any suggestion will be very helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- Thomas Piggot University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot t.pig...@bristol.ac.uk mailto:t.pig...@bristol.ac.uk
[gmx-users] '+' and '-' sign in rtp file
I had a simple query regarding the rtp file . What does the '+' and '-' sign indicates in the following dihedral inforamtion: [ dihedrals ] CA C+N+Hbackbone_prop_1 O C+N+Hbackbone_prop_2 -C NCACBbackbone_prop_3 -C NCA Cbackbone_prop_4 CA C+N +CAbackbone_prop_1 O C+N +CAbackbone_prop_1 Also, I cant understand the what is 'X' here in ffamberbon.itp: X C C X 330.33400 0.0 -30.33400 0.0 0.0 0.0 ; new99 X C O X 323.43040 0.0 -23.43040 0.0 0.0 0.0 ; new99 X C OS X 322.59360 0.0 -22.59360 0.0 0.0 0.0 ; new99 Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mdrun append problem
Hello gmxusers !! gmxcheck on #spc_25_eq.trr prints: (#spc_25_eq.trr is the renamed from #spc_25_eq.trr.1#. mdrun was stopped due to insufficient space) Checking file #spc_25_eq.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 2000.000 # Atoms 33885 Reading frame 200 time 3000.000 WARNING: Incomplete frame: nr 214 time 3070 Item#frames Timestep (ps) Step 2145 Time 2145 Lambda 2145 Coords 2145 Velocities 2145 Forces 0 Box2145 on restarting the mdrun from state.cpi mdrun -s spc_25_eq.tpr -cpi state.cpi -c spc_25_eq.pdb -o spc_25_eq.trr -e spc_25_eq.edr -g spc_25_eq.log -append yes gmxcheck on spc_25_eq.trr prints: Checking file spc_25_eq.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 2000.000 # Atoms 33885 Last frame 13 time 2065.000 Item#frames Timestep (ps) Step144.9 Time144.9 Lambda 144.9 Coords 144.9 Velocities 144.9 Forces 0 Box 144.9 It seems that the -append command didn't append. How can the appending be done. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Compiling 4.0.7 parallel fails
I had also had trouble installing gmx (paralley). But now, its solved.
I would suggest you to see that the mpi is running or not.
Here is a sample mpi C program:
#include stdio.h
#include mpi.h
int main( argc, argv )
int argc;
char **argv;
{
int rank, size;
MPI_Init( argc, argv );
MPI_Comm_size( MPI_COMM_WORLD, size );
MPI_Comm_rank( MPI_COMM_WORLD, rank );
printf( Hello world from process %d of %d\n, rank, size );
MPI_Finalize();
return 0;
}
save as mpitest.c
compile mpitest.c
mpirun -np 2 -machilefile mac a.out
If every thing is ok. Then the output will be :
Hello world from process
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Sat, Feb 6, 2010 at 5:47 AM, Jussi Lehtola jussi.leht...@helsinki.fiwrote:
On Fri, 2010-02-05 at 15:29 -0500, Matthew L. Danielson wrote:
Compiling fftw and openmpi seems to finish successfully. The serial
version of gromacs installed correctly, just when i issue --enable-mpi i
am seeing this error message (i can attached the config.log if it would
help):
checking size of int... configure: error: cannot compute sizeof (int)
From what i can get out of the mail-archive, I think this is problem
with the mpi installation or not finding the correct files etc. I have
tried re-installing openmpi (always removing the old version) using yum
(installed version 1.3.2) and installing openmpi from their website
(1.4.1). Both seem to install correctly, yet the same error message
arises when i do ./configure --enable-mpi for gromacs.
What distribution are you using? If you are running Fedora 12, you need
to load the MPI environment module with e.g.
$ module load openmpi-x86_64
Furthermore, you should have the fftw-devel and openmpi-devel packages
installed on your system.
--
--
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.leht...@helsinki.fi, p. 191 50632
--
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.leht...@helsinki.fi
--
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
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--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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[gmx-users] ATP for
Hello gmx users, I need to use ATP's parameter for amber port in gromacs. The atp.prep and frcmod.phos for ATP can be found at http://www.pharmacy.manchester.ac.uk/bryce/amber. How can I use it in ffamber. The program amb2gmx.pl needs amber to be installed, which is not present. Same with ACPYPI. Any suggestion will be very helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] error: Cannot compile and link MPI code with mpicc
Thanks.
I just added export CPPFLAGS=-I/usr/local/openmpi/include in the bashrc
file, and could compile the mpi version of gromacs.
The next thing is I got the error on executing mdrun_mpi -h
Following is the output. Kindly help.
corsica:/usr/local/gromacs/bin # mdrun_mpi -h
[corsica:17130] [NO-NAME] ORTE_ERROR_LOG: Not found in file
runtime/orte_init_stage1.c at line 182
--
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
orte_rml_base_select failed
-- Returned value -13 instead of ORTE_SUCCESS
--
--
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):
ompi_mpi_init: orte_init_stage1 failed
-- Returned Not found (-13) instead of Success (0)
--
*** An error occurred in MPI_Init
*** before MPI was initialized
*** MPI_ERRORS_ARE_FATAL (goodbye)
[corsica:17130] Abort before MPI_INIT completed successfully; not able to
guarantee that all other processes were killed!
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Mon, Feb 1, 2010 at 10:50 AM, Sarath Kumar bskumar.t...@gmail.comwrote:
Message: 5
Date: Sun, 31 Jan 2010 00:34:22 +0530
From: Chandan Choudhury iitd...@gmail.com
Subject: Re: [gmx-users] error: Cannot compile and link MPI code with
mpicc
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
4e22679c1001301104r5f1d725bjd5824e68cb3cb...@mail.gmail.com
Content-Type: text/plain; charset=iso-8859-1
Hi Ronald !!
Thanks for your reply.
I recompiled the openmpi. But while executing ./configure --enable-mpi in
gromacs4.0.7 the following error is shown in config.log file.
configure:4536: checking for mpicc
configure:4552: found /usr/lib/mpi/gcc/openmpi/bin/mpicc
configure:4563: result: mpicc
configure:4577: checking whether the MPI cc command works
configure:4601: mpicc -o conftest -g -O2 conftest.c 5
conftest.c:15:17: error: mpi.h: No such file or directory
configure:4607: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME gromacs
| #define PACKAGE_TARNAME gromacs
| #define PACKAGE_VERSION 4.0.7
| #define PACKAGE_STRING gromacs 4.0.7
| #define PACKAGE_BUGREPORT gmx-users@gromacs.org
| #define PACKAGE gromacs
| #define VERSION 4.0.7
| #define GMX_SOFTWARE_SQRT
| #define GMX_QMMM_GAUSSIAN
| #define BUILD_TIME Mon Feb 1 14:07:34 EST 2010
| #define BUILD_USER r...@corsica
| #define BUILD_MACHINE Linux 2.6.31.5-0.1-desktop i686
| /* end confdefs.h. */
| #include mpi.h
| int
| main ()
| {
| int argc; char **argv; MPI_Init(argc,argv);
| ;
| return 0;
| }
configure:4619: error: Cannot compile and link MPI code with mpicc
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Sat, Jan 30, 2010 at 10:57 PM, Roland Schulz rol...@utk.edu wrote:
Hi,
your MPI installation has to be brogen. mpicc always has to be able to
find
libmpi. Please reinstall mpi correctly.
Roland
On Sat, Jan 30, 2010 at 11:06 AM, Chandan Choudhury iitd...@gmail.com
wrote:
Hi gmx users !!
On compiling GMX paralley, following error was encountered. How can I
tackle this.
Kindly help.
checking for mpicc... mpicc
checking whether the MPI cc command works... configure: error: Cannot
compile and link MPI code with mpicc
The config.log file reads
configure:4536: checking for mpicc
configure:4552: found /usr/lib/mpi/gcc/openmpi/bin/mpicc
configure:4563: result: mpicc
configure:4577: checking whether the MPI cc command works
configure:4601: mpicc -o conftest -g -O2 -I/usr/local/openmpi/include/
conftest.c 5
/usr/lib/gcc/i586-suse-linux/4.4/../../../../i586-suse-linux/bin/ld:
cannot find -lmpi
collect2: ld returned 1 exit status
configure:4607: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME gromacs
| #define PACKAGE_TARNAME gromacs
#define PACKAGE_VERSION 4.0.7
| #define PACKAGE_STRING gromacs 4.0.7
| #define PACKAGE_BUGREPORT gmx-users@gromacs.org
| #define PACKAGE gromacs
| #define VERSION 4.0.7
| #define GMX_SOFTWARE_SQRT
| #define GMX_QMMM_GAUSSIAN
| #define BUILD_TIME Sat Jan 30 21:42:50 IST
[gmx-users] error: Cannot compile and link MPI code with mpicc
Hi gmx users !!
On compiling GMX paralley, following error was encountered. How can I tackle
this.
Kindly help.
checking for mpicc... mpicc
checking whether the MPI cc command works... configure: error: Cannot
compile and link MPI code with mpicc
The config.log file reads
configure:4536: checking for mpicc
configure:4552: found /usr/lib/mpi/gcc/openmpi/bin/mpicc
configure:4563: result: mpicc
configure:4577: checking whether the MPI cc command works
configure:4601: mpicc -o conftest -g -O2 -I/usr/local/openmpi/include/
conftest.c 5
/usr/lib/gcc/i586-suse-linux/4.4/../../../../i586-suse-linux/bin/ld: cannot
find -lmpi
collect2: ld returned 1 exit status
configure:4607: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME gromacs
| #define PACKAGE_TARNAME gromacs
#define PACKAGE_VERSION 4.0.7
| #define PACKAGE_STRING gromacs 4.0.7
| #define PACKAGE_BUGREPORT gmx-users@gromacs.org
| #define PACKAGE gromacs
| #define VERSION 4.0.7
| #define GMX_SOFTWARE_SQRT
| #define GMX_QMMM_GAUSSIAN
| #define BUILD_TIME Sat Jan 30 21:42:50 IST 2010
| #define BUILD_USER r...@shiraz
| #define BUILD_MACHINE Linux 2.6.31.5-0.1-desktop i686
| /* end confdefs.h. */
| #include mpi.h
| int
| main ()
| {
| int argc; char **argv; MPI_Init(argc,argv);
| ;
| return 0;
| }
configure:4619: error: Cannot compile and link MPI code with mpicc
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
--
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Re: [gmx-users] error: Cannot compile and link MPI code with mpicc
Hi Ronald !!
Thanks for your reply.
I recompiled the openmpi. But while executing ./configure --enable-mpi in
gromacs4.0.7 the following error is shown in config.log file.
configure:4536: checking for mpicc
configure:4552: found /usr/lib/mpi/gcc/openmpi/bin/mpicc
configure:4563: result: mpicc
configure:4577: checking whether the MPI cc command works
configure:4601: mpicc -o conftest -g -O2 conftest.c 5
conftest.c:15:17: error: mpi.h: No such file or directory
configure:4607: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME gromacs
| #define PACKAGE_TARNAME gromacs
| #define PACKAGE_VERSION 4.0.7
| #define PACKAGE_STRING gromacs 4.0.7
| #define PACKAGE_BUGREPORT gmx-users@gromacs.org
| #define PACKAGE gromacs
| #define VERSION 4.0.7
| #define GMX_SOFTWARE_SQRT
| #define GMX_QMMM_GAUSSIAN
| #define BUILD_TIME Mon Feb 1 14:07:34 EST 2010
| #define BUILD_USER r...@corsica
| #define BUILD_MACHINE Linux 2.6.31.5-0.1-desktop i686
| /* end confdefs.h. */
| #include mpi.h
| int
| main ()
| {
| int argc; char **argv; MPI_Init(argc,argv);
| ;
| return 0;
| }
configure:4619: error: Cannot compile and link MPI code with mpicc
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Sat, Jan 30, 2010 at 10:57 PM, Roland Schulz rol...@utk.edu wrote:
Hi,
your MPI installation has to be brogen. mpicc always has to be able to find
libmpi. Please reinstall mpi correctly.
Roland
On Sat, Jan 30, 2010 at 11:06 AM, Chandan Choudhury iitd...@gmail.comwrote:
Hi gmx users !!
On compiling GMX paralley, following error was encountered. How can I
tackle this.
Kindly help.
checking for mpicc... mpicc
checking whether the MPI cc command works... configure: error: Cannot
compile and link MPI code with mpicc
The config.log file reads
configure:4536: checking for mpicc
configure:4552: found /usr/lib/mpi/gcc/openmpi/bin/mpicc
configure:4563: result: mpicc
configure:4577: checking whether the MPI cc command works
configure:4601: mpicc -o conftest -g -O2 -I/usr/local/openmpi/include/
conftest.c 5
/usr/lib/gcc/i586-suse-linux/4.4/../../../../i586-suse-linux/bin/ld:
cannot find -lmpi
collect2: ld returned 1 exit status
configure:4607: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME gromacs
| #define PACKAGE_TARNAME gromacs
#define PACKAGE_VERSION 4.0.7
| #define PACKAGE_STRING gromacs 4.0.7
| #define PACKAGE_BUGREPORT gmx-users@gromacs.org
| #define PACKAGE gromacs
| #define VERSION 4.0.7
| #define GMX_SOFTWARE_SQRT
| #define GMX_QMMM_GAUSSIAN
| #define BUILD_TIME Sat Jan 30 21:42:50 IST 2010
| #define BUILD_USER r...@shiraz
| #define BUILD_MACHINE Linux 2.6.31.5-0.1-desktop i686
| /* end confdefs.h. */
| #include mpi.h
| int
| main ()
| {
| int argc; char **argv; MPI_Init(argc,argv);
| ;
| return 0;
| }
configure:4619: error: Cannot compile and link MPI code with mpicc
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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--
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
--
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Re: [gmx-users] error: Cannot compile and link MPI code with mpicc
I am using openmpi-1.4.1.
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Sun, Jan 31, 2010 at 12:34 AM, Chandan Choudhury iitd...@gmail.comwrote:
Hi Ronald !!
Thanks for your reply.
I recompiled the openmpi. But while executing ./configure --enable-mpi in
gromacs4.0.7 the following error is shown in config.log file.
configure:4536: checking for mpicc
configure:4552: found /usr/lib/mpi/gcc/openmpi/bin/mpicc
configure:4563: result: mpicc
configure:4577: checking whether the MPI cc command works
configure:4601: mpicc -o conftest -g -O2 conftest.c 5
conftest.c:15:17: error: mpi.h: No such file or directory
configure:4607: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME gromacs
| #define PACKAGE_TARNAME gromacs
| #define PACKAGE_VERSION 4.0.7
| #define PACKAGE_STRING gromacs 4.0.7
| #define PACKAGE_BUGREPORT gmx-users@gromacs.org
| #define PACKAGE gromacs
| #define VERSION 4.0.7
| #define GMX_SOFTWARE_SQRT
| #define GMX_QMMM_GAUSSIAN
| #define BUILD_TIME Mon Feb 1 14:07:34 EST 2010
| #define BUILD_USER r...@corsica
| #define BUILD_MACHINE Linux 2.6.31.5-0.1-desktop i686
| /* end confdefs.h. */
| #include mpi.h
| int
| main ()
| {
| int argc; char **argv; MPI_Init(argc,argv);
| ;
| return 0;
| }
configure:4619: error: Cannot compile and link MPI code with mpicc
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Sat, Jan 30, 2010 at 10:57 PM, Roland Schulz rol...@utk.edu wrote:
Hi,
your MPI installation has to be brogen. mpicc always has to be able to
find libmpi. Please reinstall mpi correctly.
Roland
On Sat, Jan 30, 2010 at 11:06 AM, Chandan Choudhury iitd...@gmail.comwrote:
Hi gmx users !!
On compiling GMX paralley, following error was encountered. How can I
tackle this.
Kindly help.
checking for mpicc... mpicc
checking whether the MPI cc command works... configure: error: Cannot
compile and link MPI code with mpicc
The config.log file reads
configure:4536: checking for mpicc
configure:4552: found /usr/lib/mpi/gcc/openmpi/bin/mpicc
configure:4563: result: mpicc
configure:4577: checking whether the MPI cc command works
configure:4601: mpicc -o conftest -g -O2 -I/usr/local/openmpi/include/
conftest.c 5
/usr/lib/gcc/i586-suse-linux/4.4/../../../../i586-suse-linux/bin/ld:
cannot find -lmpi
collect2: ld returned 1 exit status
configure:4607: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME gromacs
| #define PACKAGE_TARNAME gromacs
#define PACKAGE_VERSION 4.0.7
| #define PACKAGE_STRING gromacs 4.0.7
| #define PACKAGE_BUGREPORT gmx-users@gromacs.org
| #define PACKAGE gromacs
| #define VERSION 4.0.7
| #define GMX_SOFTWARE_SQRT
| #define GMX_QMMM_GAUSSIAN
| #define BUILD_TIME Sat Jan 30 21:42:50 IST 2010
| #define BUILD_USER r...@shiraz
| #define BUILD_MACHINE Linux 2.6.31.5-0.1-desktop i686
| /* end confdefs.h. */
| #include mpi.h
| int
| main ()
| {
| int argc; char **argv; MPI_Init(argc,argv);
| ;
| return 0;
| }
configure:4619: error: Cannot compile and link MPI code with mpicc
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
--
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--
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
--
gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at http://www.gromacs.org/search before
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Re: [gmx-users] decimal charge instead of integer
Hi Tom !!! Can you guide to incorporate the AMBER parameter for ATP ( http://www.pharmacy.manchester.ac.uk/bryce/amber#cof) in ffamber. I am using ffamber for the simulation of Protein + ATP. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Jan 21, 2010 at 7:06 PM, Thomas Piggot t.pig...@bristol.ac.ukwrote: If using an amber forcefield and GTP/GDP you can use the parameters on the following website. I have used the ATP/ADP ones and have had no problems with many different systems and ATP/ADP conformations with which I used to test these parameters. http://www.pharmacy.manchester.ac.uk/bryce/amber#cof Tom Justin A. Lemkul wrote: Carla Jamous wrote: Thank you Justin, but I ran a simulation before this one with GTP it worked fine. GDP GTP parameters are identical except for GDP having less atoms. This is why I can't understand why I don't get an integer charge while I did in my previous simulation. OK, but this still doesn't help anyone give you any advice. Please refer to my previous post - which case applies to you: almost integer, or way off? It is also potentially faulty logic to suggest that GDP parameters can be generated from GTP parameters by simply chopping off a phosphate. Under most force field parameter sets, the charges on the beta-phosphate will have to change since the electronic properties of the molecule are now different. -Justin Carla On Thu, Jan 21, 2010 at 2:15 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Carla Jamous wrote: Hi, In order to run my simulation, I had to insert GDP parameters in ffamber94 (the force field I'm using). However, I'm having a problem with GDP charge. the charge of every charge group in top file should be an integer. But I'm getting a decimal charge which gives me naturally a decimal total charge of my molecule. I checked number of atoms, it's correct, their charge also. But it seems it's having trouble adding charges giving an integer charge. Does anyone have an idea where is the source of the problem? What is the charge? If it is a small difference between an integer and your charge (i.e., the difference between +1. and +2) then there is no problem. The issue there is the inherent limitation of doing a lot of floating-point operations to sum the total charge. If, however, you have a charge of +1.9256 when you wanted +2, then your parameters are simply wrong. -Justin Thanks Carla -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Thomas Piggot University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] MPI ERROR while installing GMX4.0.7
Dear Nuno
thanks for your helpful suggestion. It worked successful.
But the following command mpirun -np 2 mdrun_mpi_d -v -s em_1.tpr -c
em_1.pdb doesnt seem to run parallely. I have mentiond the output below.
ban...@corsica:~/CKC/L2PJR mpirun -np 2 mdrun_mpi_d -v -s em_1.tpr -c
em_1.pdb
[corsica:17339] [NO-NAME] ORTE_ERROR_LOG: Not found in file
runtime/orte_init_stage1.c at line 182
--
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
orte_rml_base_select failed
-- Returned value -13 instead of ORTE_SUCCESS
--
[corsica:17339] [NO-NAME] ORTE_ERROR_LOG: Not found in file
runtime/orte_system_init.c at line 42
[corsica:17339] [NO-NAME] ORTE_ERROR_LOG: Not found in file
runtime/orte_init.c at line 52
--
Open RTE was unable to initialize properly. The error occured while
attempting to orte_init(). Returned value -13 instead of ORTE_SUCCESS.
--
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Fri, Jan 15, 2010 at 5:04 PM, Nuno Azoia naz...@det.uminho.pt wrote:
Hello!
I had the same problem, and for me the solution was to set up the
openmpi/lib directory. The compiler is not able to find it alone.
I'm using bash, so for me the solution was:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/your/directory/openmpi/lib
of course you have to change /your/directory with the correct path in
your system.
I hope this will help.
Nuno Azoia
On Fri, 2010-01-15 at 12:30 +0530, Chandan Choudhury wrote:
Hello gmx-users !!
I am trying to install gromacs 4.0.7 double precision with mpi. I
downloaded openmpi-1.4. and installed it.
Then executed
./configure --enable-mpi --program-suffix=_mpi_d
--prefix=/usr/local/gromacs407_double_mpi --enable-double
It showed checking for mpicc...
mpicc
checking whether the MPI cc command works...
yes
checking for catamount...
no
checking how to run the C preprocessor... mpicc
-E
checking whether mpicc accepts -O3...
yes
checking whether mpicc accepts -funroll-all-loops...
yes
checking whether mpicc accepts -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loops...
yes
checking for grep that handles long lines and
-e... /usr/bin/grep
checking for egrep... /usr/bin/grep
-E
checking for ANSI C header files...
no
checking for sys/types.h...
yes
checking for sys/stat.h...
yes
checking for stdlib.h...
yes
checking for string.h...
yes
checking for memory.h...
yes
checking for strings.h...
yes
checking for inttypes.h...
yes
checking for stdint.h...
yes
checking for unistd.h...
yes
checking whether byte ordering is bigendian...
no
checking for int...
yes
checking size of int... configure: error: cannot compute sizeof
(int)
See `config.log' for more details.
The part of the config.log reads as:
--configure:4577: checking whether the MPI cc command works
configure:4601: mpicc -o conftest -g -O2 conftest.c 5
configure:4607: $? = 0
configure:4613: result: yes
configure:4636: checking for catamount
configure:4664: mpicc -c -g -O2 conftest.c 5
conftest.c:20:2: error: #error not catamount
configure:4670: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME gromacs
| #define PACKAGE_TARNAME gromacs
| #define PACKAGE_VERSION 4.0.7
| #define PACKAGE_STRING gromacs 4.0.7
| #define PACKAGE_BUGREPORT gmx-users@gromacs.org
| #define PACKAGE gromacs
| #define VERSION 4.0.7
| #define GMX_DOUBLE
| #define GMX_SOFTWARE_SQRT
| #define GMX_QMMM_GAUSSIAN
| #define BUILD_TIME Sun Jan 17 01:26:27 EST 2010
| #define BUILD_USER r...@corsica
| #define BUILD_MACHINE Linux 2.6.31.5-0.1-desktop i686
| #define GMX_MPI
| /* end confdefs.h. */
|
| #if defined __QK_USER__
| #else
| #error not catamount
| #endif
|
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:4706: result: no
configure:5590: checking how to run the C preprocessor
configure:5630: mpicc -E conftest.c
configure:5636: $? = 0
configure:5667: mpicc -E conftest.c
conftest.c:19:28: error: ac_nonexistent.h: No such file or directory
|
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:4706: result: no
configure:5590: checking how to run the C preprocessor
configure:5630: mpicc -E conftest.c
configure:5636: $? = 0
configure:5667: mpicc
[gmx-users] MPI ERROR while installing GMX4.0.7
Hello gmx-users !!
I am trying to install gromacs 4.0.7 double precision with mpi. I downloaded
openmpi-1.4. and installed it.
Then executed
./configure --enable-mpi --program-suffix=_mpi_d
--prefix=/usr/local/gromacs407_double_mpi --enable-double
It showed checking for mpicc...
mpicc
checking whether the MPI cc command works...
yes
checking for catamount...
no
checking how to run the C preprocessor... mpicc
-E
checking whether mpicc accepts -O3...
yes
checking whether mpicc accepts -funroll-all-loops...
yes
checking whether mpicc accepts -O3 -fomit-frame-pointer -finline-functions
-Wall -Wno-unused -funroll-all-loops...
yes
checking for grep that handles long lines and -e...
/usr/bin/grep
checking for egrep... /usr/bin/grep
-E
checking for ANSI C header files...
no
checking for sys/types.h...
yes
checking for sys/stat.h...
yes
checking for stdlib.h...
yes
checking for string.h...
yes
checking for memory.h...
yes
checking for strings.h...
yes
checking for inttypes.h...
yes
checking for stdint.h...
yes
checking for unistd.h...
yes
checking whether byte ordering is bigendian...
no
checking for int...
yes
checking size of int... configure: error: cannot compute sizeof
(int)
See `config.log' for more details.
The part of the config.log reads as:
--configure:4577: checking whether the MPI cc command works
configure:4601: mpicc -o conftest -g -O2 conftest.c 5
configure:4607: $? = 0
configure:4613: result: yes
configure:4636: checking for catamount
configure:4664: mpicc -c -g -O2 conftest.c 5
conftest.c:20:2: error: #error not catamount
configure:4670: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME gromacs
| #define PACKAGE_TARNAME gromacs
| #define PACKAGE_VERSION 4.0.7
| #define PACKAGE_STRING gromacs 4.0.7
| #define PACKAGE_BUGREPORT gmx-users@gromacs.org
| #define PACKAGE gromacs
| #define VERSION 4.0.7
| #define GMX_DOUBLE
| #define GMX_SOFTWARE_SQRT
| #define GMX_QMMM_GAUSSIAN
| #define BUILD_TIME Sun Jan 17 01:26:27 EST 2010
| #define BUILD_USER r...@corsica
| #define BUILD_MACHINE Linux 2.6.31.5-0.1-desktop i686
| #define GMX_MPI
| /* end confdefs.h. */
|
| #if defined __QK_USER__
| #else
| #error not catamount
| #endif
|
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:4706: result: no
configure:5590: checking how to run the C preprocessor
configure:5630: mpicc -E conftest.c
configure:5636: $? = 0
configure:5667: mpicc -E conftest.c
conftest.c:19:28: error: ac_nonexistent.h: No such file or directory
|
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:4706: result: no
configure:5590: checking how to run the C preprocessor
configure:5630: mpicc -E conftest.c
configure:5636: $? = 0
configure:5667: mpicc -E conftest.c
conftest.c:19:28: error: ac_nonexistent.h: No such file or directory
configure:5673: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME gromacs
| #define PACKAGE_TARNAME gromacs
| #define PACKAGE_VERSION 4.0.7
| #define PACKAGE_STRING gromacs 4.0.7
| #define PACKAGE_BUGREPORT gmx-users@gromacs.org
| #define PACKAGE gromacs
| #define VERSION 4.0.7
| #define GMX_DOUBLE
| #define GMX_SOFTWARE_SQRT
| #define GMX_QMMM_GAUSSIAN
| #define BUILD_TIME Sun Jan 17 01:26:27 EST 2010
| #define BUILD_USER r...@corsica
| #define BUILD_MACHINE Linux 2.6.31.5-0.1-desktop i686
| #define GMX_MPI
| #define F77_OR_C_FUNC(name,NAME) name
| #define F77_OR_C_FUNC_(name,NAME) name
| /* end confdefs.h. */
| #include ac_nonexistent.h
configure:5706: result: mpicc -E
configure:5735: mpicc -E conftest.c
configure:5741: $? = 0
configure:5772: mpicc -E conftest.c
conftest.c:19:28: error: ac_nonexistent.h: No such file or directory
..
..
configure:6203: checking whether mpicc accepts -O3
configure:6221: result: yes
configure:6501: checking whether mpicc accepts -funroll-all-loops
configure:6519: result: yes
configure:6558: checking whether mpicc accepts -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loops
configure:6576: result: yes
configure:6668: checking for grep that handles long lines and -e
configure:6742: result: /usr/bin/grep
configure:6747: checking for egrep
configure:6825: result: /usr/bin/grep -E
configure:6830: checking for ANSI C header files
configure:6868: mpicc -c -O3 -fomit-frame-pointer -finline-functions -Wall
-Wno-unused -funroll-all-loops conftest.c 5
configure:6874: $? = 0
configure:6973: mpicc -o conftest -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loopsconftest.c 5
configure:6976: $? = 0
configure:6982: ./conftest
./conftest: error while loading shared libraries: libmpi.so.0: cannot open
shared object file: No such file or directory
configure:6985: $? = 127
configure: program exited with status 127
I also searched the gmx-users list,
Re: [gmx-users] pdb2gmx : treat CL as C
Nilesh The atom type C is for Carbon and for chlorine is Cl. So, substitute Chlorine's atom type with Cl. Chandan On Tue, Nov 17, 2009 at 9:04 AM, Nilesh Dhumal ndhu...@andrew.cmu.eduwrote: Hello, My system is having chlorin atoms. Duing pdb2gmx it treat Chlorne atoms as carbon. Can you tell me where is the problem. Is there any prblem in my pdb file Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fatal error: Atom O in residue CCMT 1 not found in rtp entry with 38 atoms while sorting atoms
Hi everyone !! I am having a problem using pdb2gmx command. Using the command on my input pdb file, it results saying Fatal error: Atom O in residue CCMT 1 not found in rtp entry with 38 atoms while sorting atoms. I do not have only O either in input pdb file or in rtp file. and its O and not 0 (zero). My part of input files reads as ATOM 1 NCCMT 1 -2.521 -2.813 2.083 0.00 0.00 ATOM 2 CA CCMT 1 -2.925 -1.739 1.166 0.00 0.00 ATOM 3 CCCMT 1 -1.711 -0.842 0.859 0.00 0.00 ATOM 4 CB CCMT 1 -4.034 -0.895 1.821 0.00 0.00 ATOM 5 SG CCMT 1 -4.523 0.408 0.710 0.00 0.00 ATOM 6 SD CCMT 1 -5.981 1.512 1.567 0.00 0.00 ATOM 7 CE CCMT 1 -7.394 0.480 1.895 0.00 0.00 ATOM 8 CZ CCMT 1 -6.988 -0.662 2.846 0.00 0.00 ATOM 9 CH CCMT 1 -7.604 -2.072 2.895 0.00 0.00 ATOM 10 CH1 CCMT 1 -8.797 -2.090 3.869 0.00 0.00 ATOM 11 CH2 CCMT 1 -8.096 -2.574 1.525 0.00 0.00 ATOM 12 CI CCMT 1 -5.986 -1.995 4.476 0.00 0.00 ATOM 13 CI1 CCMT 1 -4.582 -2.406 4.958 0.00 0.00 ATOM 14 CI2 CCMT 1 -6.931 -2.001 5.692 0.00 0.00 ATOM 15 CK CCMT 1 -6.018 -0.615 3.792 0.00 0.00 ATOM 16 NT1 CCMT 1 -6.486 -2.876 3.411 0.00 0.00 ATOM 17 OC1 CCMT 1 -0.511 -1.346 0.867 0.00 0.00 ATOM 18 OC2 CCMT 1 -1.885 0.420 0.592 0.00 0.00 ATOM 19 OT1 CCMT 1 -6.836 -4.122 3.830 0.00 0.00 ATOM 20 HCCMT 1 -1.801 -3.362 1.658 0.00 0.00 ATOM 21 HA CCMT 1 -3.292 -2.165 0.256 0.00 0.00 ATOM 22 HB1 CCMT 1 -4.878 -1.518 2.033 0.00 0.00 ATOM 23 HB2 CCMT 1 -3.668 -0.468 2.731 0.00 0.00 ATOM 24 HE1 CCMT 1 -7.754 0.067 0.976 0.00 0.00 ATOM 25 HE2 CCMT 1 -8.165 1.065 2.350 0.00 0.00 ATOM 26 HH11 CCMT 1 -9.175 -3.088 3.952 0.00 0.00 ATOM 27 HH21 CCMT 1 -8.875 -1.932 1.170 0.00 0.00 ATOM 28 HH12 CCMT 1 -8.477 -1.749 4.832 0.00 0.00 ATOM 29 HH22 CCMT 1 -7.283 -2.566 0.829 0.00 0.00 ATOM 30 HH13 CCMT 1 -9.567 -1.446 3.500 0.00 0.00 ATOM 31 HH23 CCMT 1 -8.471 -3.571 1.624 0.00 0.00 ATOM 32 HI11 CCMT 1 -4.241 -1.712 5.697 0.00 0.00 ATOM 33 HI21 CCMT 1 -6.956 -2.982 6.119 0.00 0.00 ATOM 34 HI12 CCMT 1 -4.624 -3.387 5.383 0.00 0.00 ATOM 35 HI22 CCMT 1 -6.577 -1.303 6.422 0.00 0.00 ATOM 36 HI13 CCMT 1 -3.906 -2.405 4.128 0.00 0.00 ATOM 37 HI23 CCMT 1 -7.915 -1.722 5.380 0.00 0.00 ATOM 38 HK CCMT 1 -5.391 0.221 4.019 0.00 0.00 and my part of .rtp file is [ CCMT ] [ atoms ] Namber99_34 -0.3961651 Hamber99_17 0.2951872 CAamber99_11 -0.0735013 HAamber99_19 0.1405104 CBamber99_11 -0.2213715 HB1amber99_19 0.1465376 HB2amber99_19 0.1465377 SGamber99_48 -0.2851828 SDamber99_68 -0.089 ;SM CEamber99_69 -0.10 10 HE1amber99_70 -0.09 11 HE2amber99_70 -0.09 12 CZamber99_71 -0.003 13 CHamber99_73 0.334 14 CH1amber99_74 -0.337 15 HH11amber99_76 0.090 16 HH12amber99_76 0.090 17 HH13amber99_76 0.090 18 CH2amber99_74 -0.337 19 HH21amber99_76 0.090 20 HH22amber99_76 0.090 21 HH23amber99_76 0.090 22 NT1amber99_77 0.220 23 OT1amber99_78 -0.438 24 CIamber99_75 0.329 25 CI1amber99_74 -0.337 26 HI11amber99_76 0.090 27 HI12amber99_76 0.090 28 HI13amber99_76 0.090 29 CI2amber99_74 -0.337 30 HI21amber99_76 0.090 31 HI22amber99_76 0.090 32 HI23amber99_76 0.090 33 CKamber99_72 -0.340 34 HKamber99_79 0.162 35 Camber99_20.643035 36 OC1amber99_45 -0.7981037 OC2amber99_45 -0.7981038 Any help is heartly welcomed. Thanks in advance Chandan -- Chandan kumar Choudhury NCL, Pune INDIA ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
