[gmx-users] Reg Mpi run Error

Dear Jutin and Marks  Thnak you for your previous  reply Whrn i run the following job in cluster  as follows [hinditron@compute002 gromacs-plumed-cpu-input]$ mpirun -np 8 -machinefile ~/myhosts mdrun_mpi -s CNTPEPRSOLIONSfullcputest.tpr   -v -deffnm CNTPEPRSOLIONSfull -cpt 2 I have eceived the

Re: [gmx-users] Reg Mpi run Error

On 8/31/13 4:54 AM, vidhya sankar wrote: Dear Jutin and Marks Thnak you for your previous reply Whrn i run the following job in cluster as follows [hinditron@compute002 gromacs-plumed-cpu-input]$ mpirun -np 8 -machinefile ~/myhosts mdrun_mpi -s CNTPEPRSOLIONSfullcputest.tpr -v -deffnm C

[gmx-users] Reg mpirun error

Thank you justin for your reply The error I have pasted here (also pasted in previous mail) is total screen ouptut. No further output as you stated in previous mail( The real error is further up in the screen output or in the .log file.) > [hinditron@compute002 gromacs-plumed-cpu-input]$ mp

Re: [gmx-users] Reg mpirun error

Run it again, this time re-directing stderr and stdout to files so that you can read them later. (Google for how to do that with your shell.) Mark On Sat, Aug 31, 2013 at 1:47 PM, vidhya sankar wrote: > Thank you justin for your reply > > The error I have pasted here (also pasted in previous mai

[gmx-users] grompy and how to call energy routine

Hi! I am currently using "mdrun -rerun" in order to get the energy of a system to be used in a Monte Carlo algortihm. A while ago, I was pointed to Grompy which should be capable of performing Monte Carlo using gromacs libraries (my description might not be very accurate here). I have downloa

Re: [gmx-users] grompy and how to call energy routine

After reading a bit more in the grompy directory, I found that the file __init__.py loads the necessary libraries, e.g., mdrun.so. This is because gromacs (they use version 4.0.7) was compiled with the flag --enable-shared. I am using version 4.6.3 which uses "cmake" instead of "configure". Is

Re: [gmx-users] grompy and how to call energy routine

On 8/31/13 2:16 PM, Gianluca Interlandi wrote: After reading a bit more in the grompy directory, I found that the file __init__.py loads the necessary libraries, e.g., mdrun.so. This is because gromacs (they use version 4.0.7) was compiled with the flag --enable-shared. I am using version 4.6.3

[gmx-users] question about g_hydorder

Dear all I would like to calculate angle tetrahedral order parameter of water molecules as defined by Chau et al (eq 3). I am using g_hydorder of gromacs 4.6.3 with my index group containing all oxygen atoms of water: g_hydorder -f *.xtc -s *.tpr -o file1.xpm file2.xpm -or file_1.out file_2.out -n

Re: [gmx-users] grompy and how to call energy routine

Thanks Justin. I have been wondering where I can find all options of cmake (./configure --help used to print all possible options, whereas cmake --help prints out just the usage of cmake itself). Gianluca On Sat, 31 Aug 2013, Justin Lemkul wrote: On 8/31/13 2:16 PM, Gianluca Interlandi w

Re: [gmx-users] grompy and how to call energy routine

On 8/31/13 2:32 PM, Gianluca Interlandi wrote: Thanks Justin. I have been wondering where I can find all options of cmake (./configure --help used to print all possible options, whereas cmake --help prints out just the usage of cmake itself). There's nothing like this that I'm aware of, but

Re: [gmx-users] grompy and how to call energy routine

I complied gromacs 4.6.3 with -DBUILD_SHARED_LIBS=ON. The only libraries that I find are: libmd.so libgmxana.so libgmxpreprocess.so libgmx.so which are also produced without specifying -DBUILD_SHARED_LIBS=ON There is no library called libmdrun.so like the one used in grompy. Could it be that

Re: [gmx-users] grompy and how to call energy routine

On 8/31/13 3:04 PM, Gianluca Interlandi wrote: I complied gromacs 4.6.3 with -DBUILD_SHARED_LIBS=ON. The only libraries that I find are: libmd.so libgmxana.so libgmxpreprocess.so libgmx.so which are also produced without specifying -DBUILD_SHARED_LIBS=ON There is no library called libmdrun.so

Re: [gmx-users] grompy and how to call energy routine

On 8/31/13 3:11 PM, Justin Lemkul wrote: On 8/31/13 3:04 PM, Gianluca Interlandi wrote: I complied gromacs 4.6.3 with -DBUILD_SHARED_LIBS=ON. The only libraries that I find are: libmd.so libgmxana.so libgmxpreprocess.so libgmx.so which are also produced without specifying -DBUILD_SHARED_LI

Re: [gmx-users] grompy and how to call energy routine

Thanks for looking into that. I wonder whether routines of libmd.so can be called directly from a python script just like grompy calles routines from libmdrun.so I wonder if I can find more documentation about this topic. There is a python wrapper for gromacs functions here: http://sbcb.bioch

Re: [gmx-users] grompy and how to call energy routine

On Sat, Aug 31, 2013 at 9:33 PM, Gianluca Interlandi wrote: > Thanks for looking into that. I wonder whether routines of libmd.so can be > called directly from a python script just like grompy calles routines from > libmdrun.so One could do so, but the GROMACS "libraries" are not built with this

Re: [gmx-users] grompy and how to call energy routine

Dear Mark, Thank you very much for the enlightment. I will look into named pipes. This might be appropriate since I'm calling mdrun from a TCL script in VMD. Gianluca On Sun, 1 Sep 2013, Mark Abraham wrote: On Sat, Aug 31, 2013 at 9:33 PM, Gianluca Interlandi wrote: Thanks for looking in

[gmx-users] Umbrella Sampling PMF

Hi, I ran US on an ion through a channel inserted in a bilayer. I used g_wham and got the profile output. In the visualized profile, I see a region that the plot shows a flat line and it seems the data is missed there. Would you please let me know what the reason of missing data is? Thanks