[gmx-users] g_rdf -xy

Dear Berk, I am sorry that I have a mistake in the first letter. In fact I used -bin 0.05, not 100. Yet the result is hanged. Maybe as you said, the current Gromacs can not realize what I want to do. Thanks again! H.Y. Xiao ___ gmx-users mailing

[gmx-users] g_rdf -xy

Dear gmx-users, I simulate a vapor/water/decane/vapor interface system. The interface is xy plane. I want to analysis water structure at the interface using g_rdf program along z axis with -xy parameter. But the calculation is hanged as the following: Select a reference group and 1 group Group

[gmx-users] prolems on viewing .trr file by vmd

Dear gmx-users, When I viewed the md trajactory (*.trr) of oil/water/oil system using VMD, I found the trajactories are abnormal and as if there were forces on the molecules. However, these molecules are very far. The whole simulation is normal. How to solve this problem and obtain the norm

[gmx-users] install problem

Dear gmx-users, When I parallel install gromacs-4.0.4 using my own usr. I encountered the problem. The following is my installation steps. Step 1: install lam-7.1.4 $ cd lam-7.1.4 $ ./configure --prefix=/home/xhy/software/lam-7.1.4 --without-fc --with-rsh=ssh-x

[gmx-users] parallel install gromacs-4.0.4

Dear Mark, I do not understand your meaning. Can you explain it to me again? Thanks! H.Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/se

[gmx-users] parallel install gromacs-4.0.4

Dear gmx-users, When I parallel install gromacs-4.0.4. I encountered the problem. The following is my installation steps. Step 1: install fftw-3.1.2 # cd fftw-3.1.2 # ./configure --enable-float --enable-mpi -enable-threads # make # make install Step 2: ins

[gmx-users] minimization problem

Hi, I has used the periodic boundary conditions and correct em.mdp file. However, the minimized result is water/decane/water, while I set decane/water/decane as the initial system . I cannot understand the reason. Please give me some constructive suggestion! Thanks! H. Y. Xiao _

[gmx-users] minimization problem

Hi, David van der Spoel I used the periodic boundary conditions. The box is 3.006x3.002x6.000 along x,y,z direction,respectively.The following is the em.mdp file. ; ; User xiao ; 2008.9.28 10:23 ; Input file ; cpp = /usr/bin/cpp define = -DFLEXI

[gmx-users] minimization problems

Hi, gmx-users, I built a system,decane(42molecule)/water(903)/decane(42), including the two decane/water interfaces. However, when I minimized this system, I found the system turn into water/decane(84)/water. That is to say in the initial system two parts of decane turn into a part, while wate

[gmx-users] error range of surface tension

Hi all, I simulated the water/air system and calculated the surface tension of water by using g_energy. The following is the result: Statistics over 51 steps [ 1000.0001 thru 2000.0001 ps ], 1 data sets All averages are exact over 51 steps Energy Average RMSD

[gmx-users] Different potential function combination

Hi, all gmx-users, I am simulating the surfactant on the liquid/liquid interface. After reading a lot of paper, I predefine the different potential function forms for these three parts (surfactant, water, CCl4). For water model, I used the SPC model; for CCl4, I used the function form from gro

[gmx-users] charge distribution

Dear Justin, For sodium dodecylbenzenesulfonate(C12H25C6H4SO3Na), the charges of S and O in S03- , I cannot find the suitable charge. Forthermore, the carbon in benzene connecting the SO3- is setted to be zero, I think that there may be questionable. The polarization of SO3- is very large. what

[gmx-users] charge distribution

Hi, gmx-usrs, I want to ask for a problem on the charge distribution. I simulate the sodium dodecylbenzenesulfonate and its homologues in solution using the gromos96 force field. I can not find the similar atom type as replace in the gromos96 force field . How do I define every atomic charge? I

[gmx-users] surface simulation

Hi, Mark Abraham, I accepted your suggestion on the language. I simulated the CCl4 surface system. In order to simplify model, using the vacuum replaced the gas phase. Furthermore, I found some paper by other people also deal with the gas/liquid using the vacuum. In vacuum/CCl4, can I contr

[gmx-users] CCl4 parameters

Hi, Justin, This is my CCl4.top file. ; ; File 'ccl4.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Thu Oct 9 08:18:55 2008 ; ; This is your topology file ; "God is a DJ" (Faithless) ; ; Include forcefield parameters #include "ffG53a

[gmx-users] CCl4 parameters problem

Hi, all gmx-users, I obtained the gromos96.1 itp file of CCl4 from the PRODRG program and I modified it to agree with the ffG53a6.itp force field parameters. Please see the following, [ moleculetype ] ; Name nrexcl CL4 3 [ atoms ] ; nr type resnr resid atom cgnr charge

[gmx-users] surface simulation

Hi, all gmx-users, I was simulating a CCl4 surface system. I encounter some problems. I hope for your help. First I built a 3x3x3 nm3 CCl4 box, then solved it into a 3x3x15 box in order to form gas/CCl4/gas surface system. After simulating in NVT, two CCl4 molecules run away to the gas phas