Re: [gmx-users] gromacs error

Make sure you have libfftw3f installed properly. In such case command:whereis libfftw3fshould give you location of that file which gmx is unable to find. On Saturday, August 26, 2017, 1:13:38 PM GMT+3, Neha Gupta wrote: Hi gromacs users, How to fix this error? gmx:

Re: [gmx-users] QM/MM simulation (Mostafa Javaheri)

Hi, Could it be that the QM level of theory is not suited (candidates are charge and multiplicity) for the QM subsystem? What happens if you run a QM only calculation on your QM system ? Gerrit Dear gmx users I'm doing an QM/MM simulation of a ligand-protein system by the Gromacs ORCA

Re: [gmx-users] Trouble with gmx distance

Two atoms for distance calculation have to be in same selection thus program expects even number of positions and do not get in my opinion.You could show your index.ndx for better investigation. On Monday, August 21, 2017, 9:24:35 PM GMT+3, Sotirios Dionysios I. Papadatos

Re: [gmx-users] ERROR IN EXECUTION ---GMX

Hi, I gave these commands initially PATH=$PATH:"/usr/local/gromacs/bin/" (this mentions path to gmx) LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"/usr/local/gromacs/share/gromacs/top" For that, I got the response, gmx: error while loading shared libraries: libfftw3f.so.3: cannot open shared object

Re: [gmx-users] Unable to install 5.1.14

You have updated boost so you have to update GROMACS too. 2016.3 is the latest version you should download it. Another possibility is to downgrade boost to older, but you can bump into other mish-mash issues. I do not recommend that. On Sunday, August 27, 2017, 11:36:21 PM GMT+3, Rajat

Re: [gmx-users] ERROR IN EXECUTION ---GMX

If you are using linux and gromacs is installed in /user/local/bin check these steps vi ~/.bashrc in the last line of the file add source /usr/local/bin/GMXRC and save this. On Mon, Aug 28, 2017 at 12:08 PM, Neha Gupta wrote: > Hi, > > I gave these commands

Re: [gmx-users] Performance values

On Mon, Aug 7, 2017 at 6:10 PM, Maureen Chew wrote: > Szilárd, > Thank you so very much for the reply!You mention > that time/step is important if trying to do an apples-to-apples > comparison for any given simulation. > > I have a few questions - For specific

Re: [gmx-users] Error with MPICH

That kind of cmake invocation with MPI on without setting the compilers to the MPI wrappers can often fail depending on how well the MPI installation is detected by cmake. Try setting CMAKE_C_COMPILER and CMAKE_CXX_COMPILER variables to the MPI compiler wrappers, i.e. mpicc/mpic++ or similar. --

Re: [gmx-users] Trouble with gmx distance

Wow! It worked!!! Thank you so much. It just needed to pass both choices in one line. Thanks again. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Vytautas Rakeviius

[gmx-users] problem installing plumed-2.3.2

Hii all    I am trying to install plumed-2.3.2 in CRAY system. I am using this command to configure plumed  ./configure --enable-mpi --prefix=/work/plumed-2.2.5/ At the end it shows a warning  configure: WARNING: PLUMED will NOT be compiled using MPI because MPI have not been found!

Re: [gmx-users] problem installing plumed-2.3.2

Hi, please post these questions to plumed mailing list. You should check the name of your MPI compiler and pass it to configure as CXX=name/of/the/compiler Giovanni On Mon, Aug 28, 2017 at 3:36 PM, wrote: > Hii all >I am trying to install plumed-2.3.2 in CRAY system. I

[gmx-users] Corrupted checkpoint file from MD simulation

Hi everyone, Recently, I was running a simulation on a computer cluster, but the computer cluster unexpectedly crashed. The trajectory file (.xtc) was saved, but the checkpoint files (both .cpt and _prev.cpt) seem to be corrupted. Does anyone have any recommendations on continuing the trajectory

Re: [gmx-users] Corrupted checkpoint file from MD simulation

Hi, if you have .trr with saved velocities (at least from time to time), you can create new tpr file starting with the last frame you have. Command: gmx tpbconv -s .tpr -f .trr -e .edr -time -o .tpr And with this new .tpr you'll start normal run (gmx mdrun ...) and than you have to

[gmx-users] Surface Tension Calculation

Hi, gmx users, I have some questions regarding the surface tension calculation in gromacs. I was running simulations about interface between phase 1 (solid) and phase 2 (liquid). In my production run, the phase 1 molecules are frozen and I need to calculate the interfacial tension between phase 1

Re: [gmx-users] RDF

No idea what a surface distribution function is, and how it is generated. But I suspect that those two are not the same. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052

[gmx-users] nstcomm < nstcalenergy

Dear every user, I am using Andersen thermostat and nstcomm should be set to 1 (step). However, after specifying nstcomm = 1, an error has returned - nstcalenergy cannot be smaller than nstcomm. GROMACS automatically sets it to nstcalenergy step. I fail to search for "nstcalenergy" in neither

Re: [gmx-users] gromacs error

Hi Vytautas, Thank you for your response.. I did as you told and got this message at the command prompt libfftw3f: /usr/local/lib/libfftw3f.la /usr/local/lib/libfftw3f.a But the error tells me : gmx: error while loading shared libraries: libfftw3f.so.3: cannot open shared object file: No such

[gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc

Dear All, I've carried out a 100ns simulation of protein in water and want to calculate hydrogen bond (forward) lifetime between Protein-Water. Initially, I thought it would be better to analyse hydrogen bonds in last 60ns of simulation, so I truncated the trajectory using g_trjconv using -b 4