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If you get errors on linking such as

/home/..../Library/Gromacs/versions/serial-4.5.5/lib/libgmx.a(vmddlopen.o): In function `vmddlclose': vmddlopen.c:(.text+0x1): undefined reference to `dlclose'
...
/home/..../Library/Gromacs/versions/serial-4.5.5/lib/libgmx.a(pthreads.o): In function `tMPI_Thread_key_delete': pthreads.c:(.text+0x5e6): undefined reference to `pthread_key_delete'

then that means that you have to add additional options to the CPPFLAG and especially LDFLAG variables in the Makefile:

• add -pthread
• add the dl library

The lines in the Makefile are:

 CPPFLAGS += -I$(INCLUDEDIR) -I$(GMX_INCLUDE_DIR) -pthread
 LDFLAGS  +=  -pthread -lm -ldl -L$(GMX_LIB_DIR) -lmd -lgmx

Dear all,

Whenever I try to use g_ri3Dc in GROMACS version 4.5.7 with options:

g_ri3Dc -f hyper_MD.trr -s hyper_MD.tpr -n hyper.ndx -R 13.5 -z1 -15 -z2 15 -b 1000 -e 150000

I get the following error:

Writing 3D density grid with header
{T}149100ps{grp}CHAIN{z1}-15.00{z2}15.00{Rmax}13.50{}0.050{}6655.11{XTC}hyper_MD.trr{Delta}(0.050,0.050,0.050){sumP}9.92277e+08ps

grid_write(): XDR write failed.
Writing the 3D grid failed.

An output file is being created, it contains the header line and some unreadable characters.
I have also tried several other options with no discernible improvements. It seems something is wrong with XDR, but I have no idea what could be the issue. Could you help me?

Thank you in advance,
Jaap

I noticed that the rdf calculated by a_ri3Dc is not weighted by radius so it calculates this:

P(r) = 1/Lz 1/2pi  Int dphi dz n(r,phi,z)

not

P(r) = 1/Lz 1/2pi r Int dphi dz n(r,phi,z)

(A Ghavami via email)

(From an email by albumns)

I noticed that the water distribution along XZ direction is symmetric, but my protein is not symmetric. I cannot understand why I got such results, although the water density along Z direction looks all right.

Here is the steps I used for the water density calculation in GridCount:

grompp -f md.mdp -c npt4.gro -o md.tpr
g_ri3Dc -f md.xtc -s md.tpr -n .index.ndx -grid gridxdr.dat # (I select solvent in this pop up dialogue ) 
a_ri3Dc -grid gridxdr.dat -profile profile.xvg -xyp xyp.dat -xzp xzp.dat -yzp yzp.dat -rzp rzp.dat -rdf rdf.xvg -zdf zdf.xvg -lzdf lzdf.xvg -hxyp hxyp.dat -hrzp hrzp.dat -hrdf hrdf.xvg -dump gridasc.dat

Then I plot the data with new generated file: hrzp.dat and found that it the water density along non-Z directory is symmetric as illustrated in attached figure.

So I am just wondering why it is symmetric even my protein is not symmetric in that direction?

Currently gridcount does not compile against Gromacs 4.6.x (or 5.x)

With 4.6.5 the first error is

g_ri3Dc.c:107:21: error: rdgroup.h: No such file or directory
make[1]: *** [g_ri3Dc.o] Error 1

Karim Mahnam (via email)

I want to calculate 3D density of ions around my protein via gridcount.
I have installed and configured Gromacs 4.5.3 with "--enable-shared" option.
I compiled and installed gridcount-gridcount-gmx-4.5.1.4 without any error and it make g_ri3Dc and a_ri3Dc bineries in /usr/local/gromacs/bin , but when I want to run g_ri3Dc or a_ri3Dc, it says "command not found" or when I run it in bin directory of gromacs it says "error while loading shared libraries: libmd.so.6: cannot open shared object file: No such file or directory"

Would you please tell me how can i solve this problem and how can obtain 3D density of ions around my protein.