[gmx-users] Weeks Chandler Andersen potential

Hi all,  I want to simulate something and want to use Weeks Chandler Andersen potential.  http://matdl.org/matdlwiki/index.php/softmatter:Weeks-Chandler-Andersen_Potential (http://matdl.org/matdlwiki/index.php/softmatter:Weeks-Chandler-Andersen_Potential) Is table option the only way to go ? 

[gmx-users] surface tension calcualtion

Hi all, Can someone comment if the method I am following is correct: I want to calculate surface tension of a liquid, I simulate a thin film of the liquid periodic in x-y and I expand the z periodic boundaries. Then I use g_energy (surface tension) to calculate the value and divide it

[gmx-users] Epsilon AA, Epsilon AB, Epsilon BB

Dear all, I want to use a system in which Epsilon AA = 1 and Epsilon BB = 0.5. But I want to use Epsilon AB = 1.5. How do I do that in gromacs? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] External forces

Hi all, Can anyone tell me how I can impart external forces on a system - say I have a water droplet placed on a tilted polymer surface. With the application of the force, the droplet should flow. - Rohit -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] g_cluster

Hi All, Greetings !I have a question about g_cluster. I have a configuration of Lennard Jones particles. For each particle I calculate an individual bond orientational order parameter Q4. Based on this order parameter I want to calculate the clusters in the system. Meaning - particles connected

[gmx-users] Coarse graining for Benzene and related molecules

! __ Rohit Malshe 1112, Engineering Hall Tel :001 608 262 3370 Graduate Student

[gmx-users] glass transition temperature

Hi all, I have a molecule-model who's diffusivity data is available with me. Is there a way I can calculate glass transition temperature for this model from the Diffusivity data ? I do not want to perform glass transition temperature calculations. I know it can be calculated from WLF

[gmx-users] Table potential example

for similar framework. Any help is deeply appreciated. __ Rohit Malshe 1112, Engineering Hall Tel :001 608 262 3370

[gmx-users] gromacs to DLPOLY

. __ Rohit Malshe 1112, Engineering Hall Tel :001 608 262 3370 Graduate Student

[gmx-users] Library file ffG43a1.n2t not found

Hi all, I was trying to use x2top to generate a topology file, but I got following error when I selected a forcefield type. Library file ffG43a1.n2t not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) Please let me know

[gmx-users] Mean squared displacement for fast moving particles

any one know how should I proceed ? I have the topology, and trajectories already generated. Rohit Malshe ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] Topology of tris-Naphthyl-Benzene

Hi all ! Does anyone have the topology and coordinates of tris-naphthyl-benzene in bulk ? I would be highly grateful if someone can share those with me. Thanks a lot in advance. __ Rohit

[gmx-users] scripting for gromacs ?

Hi all, I use Linux - fedora Core 6 and I use gromacs to do some trjconv operations. I have a shell script to be run in different folders. The script runs a command -- trjconv -f input.gro -pbc whole -o out.gro and comes to following point. Opening library file

[gmx-users] C500 Configuration and parameters help

Hi all, I am in need of simulating C500 molecules in bulk. 1 Particles is a good number for me for testing some order parameter codes. Does anyone have relevant .gro, .itp, .mdp, .top files for the same ? It will be a great help. ~ Rohit