[gmx-users] interaction energy

 HI I'm simulating gold-protein interaction by gromacs. after MD simulation I want to calculate interaction energy of each aminoacids with AU surface.  Enon-bond = E(vdw) + E(elec) gold atoms  charge in simulation were considered 0, then E non-bonded=E(vdw) Is this true? The interaction

[gmx-users] Plotting data from g_spatial

Dear users I have a question regarding the cube file output we get from g_spatial analysis. My system comprises of hundreds of ionic liquids (composed of cation and anion). If I would like to see the spatial distribution of anions around cation, how do I get an average distribution. E.g, the way

[gmx-users] installing gromacs-4.6.1 with CMake

Hi. I'm trying to build a build with cmake-2.8.10.2-linux for 'gromacs-4.6.1' as the build target. First, I extracted gromacs-4.6.1.tar.gz and, create a new folder; build inside the extracted folder. Then, inside build folder, I configured using CMake. $ tar -xvzf gromacs-4.6.1.tar.gz $ cd

[gmx-users] Regarding top2psf script

Dear all, I want to reverse transform my CG lipid system to AA. I have been using g_fg2cg but I am getting some errors (like Atoms in the .top are not numbered consecutively from 1). So, I intend to use the script top2psf.plwritten by Dr.Lemkul, so that I can avail the help of VMD in cg2aa

Re: [gmx-users] interaction energy

On 4/18/13 2:00 AM, fatemeh ramezani wrote: HI I'm simulating gold-protein interaction by gromacs. after MD simulation I want to calculate interaction energy of each aminoacids with AU surface. Enon-bond = E(vdw) + E(elec) gold atoms charge in simulation were considered 0, then E

Re: [gmx-users] installing gromacs-4.6.1 with CMake

On 4/18/13 3:09 AM, 中野佑香 wrote: Hi. I'm trying to build a build with cmake-2.8.10.2-linux for 'gromacs-4.6.1' as the build target. First, I extracted gromacs-4.6.1.tar.gz and, create a new folder; build inside the extracted folder. Then, inside build folder, I configured using CMake. $

Re: [gmx-users] Regarding top2psf script

On 4/18/13 5:15 AM, Venkat Reddy wrote: Dear all, I want to reverse transform my CG lipid system to AA. I have been using g_fg2cg but I am getting some errors (like Atoms in the .top are not numbered consecutively from 1). So, I intend to use the script top2psf.plwritten by Dr.Lemkul, so that

[gmx-users] Applying a Lennard-Jones Gauss potential function for TIP5P water

Greetings, I am simulating a box of TIP5P waters and I would like to know if it is possible to change the standard LJ potential function to a more complex one (LJ-Gauss), while keeping the coulombic interaction standard. The custom potential will act between the oxygen atoms only and has the

Re: [gmx-users] Applying a Lennard-Jones Gauss potential function for TIP5P water

On 4/18/13 7:31 AM, Andrish Reddy wrote: Greetings, I am simulating a box of TIP5P waters and I would like to know if it is possible to change the standard LJ potential function to a more complex one (LJ-Gauss), while keeping the coulombic interaction standard. The custom potential will

Re: [gmx-users] installing gromacs-4.6.1 with CMake

Dear Justin, Thank you for your fast reply. cmake was successfully worked after I removed CMakeCache.txt from gromacs-**4.6.1 directory and corrected CMake path in .tcshrc . Thank you! -Yuka 2013/4/18 Justin Lemkul jalem...@vt.edu On 4/18/13 3:09 AM, 中野佑香 wrote: Hi. I'm trying to

[gmx-users] Re: Applying a Lennard-Jones Gauss potential function for TIP5P water

Thanks Justin, I had a look at the manual regarding tabulated potentials... for clarity, The table values must contain: x, f(x), −f(x), g(x), −g(x), h(x), −h(x). For my function then would f(x) = 1/r g(x) = eps*[(sig/r)^12 - 2*(sig/r)^6] and h(x) = -epsG*[exp-(((r-rG)^2) / (2*sigG^2))] ?

[gmx-users] Running simulation over openmpi in rsh

Dear Gmx, Is there anyway I can run simulation using mpirun command via rsh? I am using openmpi 1.6 version. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

[gmx-users] How to fix interfacial tension in NPT

Dear Gromacs users, I have runned a semiisotropic NPT simulation for a membrane, I have fixed the pressure in x and y axis and I varied it only in z axis to keep a stable interface. But after simulation the obtained interfacial tension is far bigger than the experimental value. Experimental is 27

[gmx-users] Membrane Simulation

Dear all I'm trying to start a simulation with a protein embedded in a bilayer of POPC molecules, but I have some problems when I pack the lipids around the protein. Infact I place the protein in the proper position using the editconf tool with the “-rotate” and “-center” options on, but when

[gmx-users] ffnonbonded value of charmm to charmm27 ff

Dear gmx, I m having a confusion of using the literature value of non-bonded ( charmm format) to use in gromacs over charmm27.ff ? For example, the literature reported the Carbon nonbonded as ( sigma =3.83, epsilon -0.0262 ), whereas the charmm27.ff in gromacs- ffnonbonded value listed for

RE: [gmx-users] Building Single and Double Precision in 4.6.1?

Thanks for the reply, so the next question, after I finish building single precision non parallel, is there an efficient way to kick off the double precision build, then the single precision mpi and so on? Or do I need to delete everything from my build directory before running cmake again?

Re: [gmx-users] Building Single and Double Precision in 4.6.1?

On Thu, Apr 18, 2013 at 6:17 PM, Mike Hanby mha...@uab.edu wrote: Thanks for the reply, so the next question, after I finish building single precision non parallel, is there an efficient way to kick off the double precision build, then the single precision mpi and so on? Or do I need to

Re: [gmx-users] Re: Applying a Lennard-Jones Gauss potential function for TIP5P water

On 4/18/13 8:44 AM, Andrish Reddy wrote: Thanks Justin, I had a look at the manual regarding tabulated potentials... for clarity, The table values must contain: x, f(x), −f(x), g(x), −g(x), h(x), −h(x). For my function then would f(x) = 1/r g(x) = eps*[(sig/r)^12 - 2*(sig/r)^6] and h(x) =

Re: [gmx-users] How to fix interfacial tension in NPT

On 4/18/13 10:51 AM, Souilem Safa wrote: Dear Gromacs users, I have runned a semiisotropic NPT simulation for a membrane, I have fixed the pressure in x and y axis and I varied it only in z axis to keep a stable interface. But after simulation the obtained interfacial tension is far bigger

Re: [gmx-users] Membrane Simulation

On 4/18/13 10:59 AM, Giuseppe wrote: Dear all I'm trying to start a simulation with a protein embedded in a bilayer of POPC molecules, but I have some problems when I pack the lipids around the protein. Infact I place the protein in the proper position using the editconf tool with the

[gmx-users] Free energy on GPU?

Dear all. I'm trying to estimate relative solvation enegry of brombenzene (relative to benzene) via thermodynamic integration. Can I perform such calculation in GROMACS with GPU acceleration? As I currently understand to make use of GPU one need to use Verlet cutoff scheme. When I do so with pme

Re: [gmx-users] Free energy on GPU?

On 4/18/13 2:30 PM, Олег Титов wrote: Dear all. I'm trying to estimate relative solvation enegry of brombenzene (relative to benzene) via thermodynamic integration. Can I perform such calculation in GROMACS with GPU acceleration? As I currently understand to make use of GPU one need to use

Re: [gmx-users] ffnonbonded value of charmm to charmm27 ff

Identify the equations into which they are inserted. Apply scaling parameters to change the units. Learn to check others' work before investing months of effort ;-) Mark On Thu, Apr 18, 2013 at 5:39 PM, 라지브간디 ra...@kaist.ac.kr wrote: Dear gmx, I m having a confusion of using the literature

Re: [gmx-users] Autocorrelation of C-N

Chapter 8 is your friend. Find a tool to feed data to g_analyze. Mark On Wed, Apr 17, 2013 at 4:23 PM, Steven Neumann s.neuman...@gmail.comwrote: Dear Users, Could you advise me please how to calculate vector C-N autocorrelation function in my protein along the simulation time? Steven

Re: [gmx-users] Running simulation over openmpi in rsh

No idea. Configuring your MPI system is not really on topic for the GROMACS mailing list. I suggest you read your OpenMPI documentation. Mark On Thu, Apr 18, 2013 at 2:58 PM, 라지브간디 ra...@kaist.ac.kr wrote: Dear Gmx, Is there anyway I can run simulation using mpirun command via rsh? I am

[gmx-users] pdb2gmx for small molecules?

Hi, I'm not clear on how to use pdb2gmx to set up a small molecule for simulation, or perhaps the limitations on this capability. My understanding from the latest documentation and the 2013 publication is that v4.5 is capable of handling non-protein/nucleic acid as input. I

Re: [gmx-users] pdb2gmx for small molecules?

On 4/18/13 3:32 PM, Warren Gallin wrote: Hi, I'm not clear on how to use pdb2gmx to set up a small molecule for simulation, or perhaps the limitations on this capability. My understanding from the latest documentation and the 2013 publication is that v4.5 is capable of handling

Re: [gmx-users] pdb2gmx for small molecules?

On 2013-04-18 21:35, Justin Lemkul wrote: On 4/18/13 3:32 PM, Warren Gallin wrote: Hi, I'm not clear on how to use pdb2gmx to set up a small molecule for simulation, or perhaps the limitations on this capability. My understanding from the latest documentation and the 2013 publication is

[gmx-users] Announcement: new version of GridMAT-MD available

Greetings all, I wanted to announce that we have released version 2.0 of GridMAT-MD. Many of you use this program for membrane analysis and I am pleased to note that we have introduced many new features based on your feedback, including trajectory support (multi-frame .pdb and .gro files).

[gmx-users] A beginner's question ...

Dear All I am new to GROMACS, I have the following question: What is the difference between Pres. DC and Pressure in g_energy analysis ? Thanks in advance Venkatesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the

Re: [gmx-users] A beginner's question ...

On 4/18/13 7:22 PM, Venkatesh Ramakrishnan wrote: Dear All I am new to GROMACS, I have the following question: What is the difference between Pres. DC and Pressure in g_energy analysis ? Pres. DC is the correction applied to the pressure term in dispersion correction when using DispCorr

[gmx-users] Different energy using the identical tpr file

Hello, I have a 2 tpr files which are identical. Then I am doing a single step MD (I put n_step=0) simulation just to compute the total energy of a certain configuration. These tpr files give me different energy values ... when I run it on my computer or on another computer. Even the gromacs

Re: [gmx-users] Announcement: new version of GridMAT-MD available

It seems to be good. However, I always have problem to compile matpack which is needed by xmatrix... I sent the author an email, but never replied.. here is the log file: creating libpng12.la (cd .libs rm -f libpng12.la ln -s ../libpng12.la libpng12.la) make[4]: Leaving directory