[gmx-users] Use the TIP4P water model in the gmx2 force field

 Hello, I want to use the tip4p water model in the gmx2 force field, but it seems that it doesn't have the nobond parameter of the OWT4 in the gmx2 force field ,does it need add by myself?   look  forward to your respond. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.o

[gmx-users] install problem of ngmx.

Hello, I installed the gromacs4.0.5, when I made, it had lots of mistakes, below is some of the mistakes: In file included from ngmx.c:50: Xstuff.h:48:22: error: X11/Xlib.h: No such file or directory Xstuff.h:49:23: error: X11/Xutil.h: No such file or directory Xstuff.h:51:28: error: X11/cursorf

[gmx-users] hou to Construct the oil/water interface

 Hello, I want to construct the oil/water interface, like this: X and Y axises of the box are 5 nm, Z axis is 10 nm. 0-5 nm of Z axis in the  box is water, and 5-10 nm of Z axis in the box is oil (for example :dodecane), how can I achieve the aim?   Thank you very much!     --

[gmx-users] How to deal with the top files

 Hello，I have one box,which has two kinds of  solvents and two kinds of solutes. How can I  put  the infermation  of them in one top fles, or what shall I do  to Setup the energy minimization, for the infermation is not in the same top file ?   Thank you !  -- gmx-users mailing listgmx-use

[gmx-users] isntall problem of ngmx

 Hello, I have done the ./configure --without-X,why it still would compile the ngmx? I had posted to you that it would make errores  if compiled the ngmx. the errores are like this : In file included from ngmx.c:50: Xstuff.h:48:22: error: X11/Xlib.h: No such file or directory Xstuff.h:49:23: erro

[gmx-users] install problem of ngmx

Hello,  my configure line is ./configure --without-X  --enable-mpi --enable-fortran --prefix=/mnt/soft/chemtec/gromacs4.0.5. I have been setted  in the ~/.bashrc like this :   export PATH=/opt/mpich2wgs/bin:$PATH:/share/apps/intel/fce/10.1.022/bin export CC=gcc export CXX=g++ export CFLAGS="-03 x

[gmx-users] install problem of ngmx

Hello, the error is like that : *In file included from ngmx.c:50:* > > *Xstuff.h:48:22: error: X11/Xlib.h: No such file or directory* > > *Xstuff.h:49:23: error: X11/Xutil.h: No such file or directory* > > *Xstuff.h:51:28: error: X11/cursorfont.h: No such file or directory* > > *Xstuff.h:52:27: err

[gmx-users] How to change the resname?

Hello, first, I make a grateful acknowledgement for Mark and Justin's help to guide me to install the gromacs,I have installed it well. I have another question need you help , could I change the resname in the .gro and .top or .itp documents? if yes, how shall I do, just change it ?   Thank you

[gmx-users] How to set the density of the box?

  Hello, I want to set the density of the box (e.g. set 1 g/ml for the water box). I use the density option in the editconf, then use the genbox to generate the box, but the result of the density is not what I setted. How can  I do ?   I have another question, I don't find the tip3p.gro

[gmx-users] TIP3P water box

 Hello,I want to  use spc216.gro and apply the tip3p.itp parameters, but it would make a mistake for the pre-processor "grompp" ,it said can't find HW atomtypes, the force file which I used is "ffG43a1.itp". my tip3p.itp file is as follows:   [ moleculetype ] ; molname nrexcl SOL  2 [ atoms ] ;

[gmx-users] How to use the walls

Hello, I had posted this message yesterday,maybe it was missing.I want to use the wall for 2d periodic boundary, but I don't know how to set the wall_type and wall_density, I don't know what thay depend on for setting. I also want to know the format of them for setting.   Thank you !-- gmx-u

[gmx-users] warning when process the files with grompp

 Hello, I want to generate the em.tpr file, but  it arise the warning like this : Warning: atom name 1 in TBP_wat.top and 10tbpc12wat1.gro does not match (C13 - OW) Warning: atom name 2 in TBP_wat.top and 10tbpc12wat1.gro does not match (C10 - HW1) Warning: atom name 3 in TBP_wat.top and 10tbpc1

[gmx-users] the error for 2D periodic boundary

 Hello,  when I use the 2D periodic boundary for the pr run , it just ran several steps then exited,  the log file has some error message like this : Program mdrun, VERSION 4.0.5 Source code file: nsgrid.c, line: 357 Range checking error: Explanation: During neighborsearching, we assign each part

[gmx-users] the problem of the periodic boundary

Hello, I use the 2D periodic boundary along the x and y axises, it has a strange thing. my solvent is dodecane,  I view the output  trajectory in the VMD, for one molecule, it has some part in the left(top), and some in the right(bottom), it still connections to each other, how to solve this pr

[gmx-users] calculate interfacial tension

Hello, I want to calculate the interfacial tension of the oil/water interface . I use 2D periodic boundary along Z axis , I get the interfacial teision from the .edr file (namely #Surf*SurfTen), it seems that the Surf*SurfTen is the total tension  of the two interface ,is it that ?  Does it has

[gmx-users] the broken of the molecules

 Hello, I do the energy minimization of the butylene box , but some butylene molecules are broken after that. The butylene itp file is produced by PRODRG, as follows:   [ moleculetype ] ; Name nrexcl BUT  3 [ atoms ] ;   nr  type  resnr resid  atom  cgnr   charge mass 1   C