[gmx-users] Constant velocity group

Dear all, Is there a way to impart a constant velocity to a group during a simulation. That is irrespective of any interaction the velocity will remain same during the course of the simulation. -- Avinash Kumar. ___ gmx-users mailing list

[gmx-users] Constant Velocity

Hello all, Is there anyway to provide constant velocity to any particular group of atoms.? -- Avinash Kumar. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] pull code

Hello all, does anybody possess a sample of "pull.pdo" data file for pull codes. -- Avinash Kumar. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archi

[gmx-users] Carbon tetrachloride

Hello all, Does anybody have a .gro and .pdb containing carbon tetrachloride? I am having problems generating the .pdb as the conversion to gro is not taking place correctly? Thank you -- Avinash Kumar. ___ gmx-users mailing listgmx-users

[gmx-users] liquid vapour

Hello all, I am working on liquid vapour interfaces. How do I determine which atom is in vapour state and which one in liquid. What thermodynamics property will tell me that? Thank you. -- Avinash Kumar. ___ gmx-users mailing listgmx-users

[gmx-users] Pressure componets

Dear All, I wish to calculate the components of pressure (pressure tensor) of a group, ie x,y and z components . Is there any any function in GROMACS which will do it for a group as a function of height. Or do I have to write my own code for postprocessing. Thank you. -- Avinash Kumar

[gmx-users] calculating surface tension

mand prompt or where ? -- Avinash Kumar. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requ

[gmx-users] pressure component

Dear All, I wish to calculate the components of pressure (pressure tensor) of a group, ie x,y and z components . Is there any any function in GROMACS which will do it for a group as a function of height. Or do I have to write my own code for postprocessing. Thank you. -- Avinash Kumar

[gmx-users] wall modelling

. -- Avinash Kumar. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the

[gmx-users] Changing source code of GROMACS

Hello all, I am trying to change the source code of GROMACS. Can somebody assist me on this? I mean how to do this,and where actually the changes have to be made so that software works in a modifies manner. ___ gmx-users mailing listgmx-use

[gmx-users] source code

Hello all, I am trying to change the source code of GROMACS. Can somebody assist me on this? I mean how to do this,and where actually the changes have to be made so that software works in a modifies manner. Avinash ___ gmx-users mailing list

[gmx-users] source code change

Hello all, Thank you Xavier for your reply. I will explain why I want to change the source code. I have to implement a modified Lennard Jones potential, ⎧ ⎪ ⎨ 4 *epsilon{( _σ_ )^12 − (_σ_ )^6} − VLJ (rc ), r ≤ rc , r

[gmx-users] Modified Lennard Jones potential

ease guide me on this. Avinash Kumar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe reque

[gmx-users] source code change

To Maik Goette, Thank you for your reply. Avinash Kumar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't

[gmx-users] potential tables not working

where my other files are and "s1" and "s2" are name of the groups. Thanks in advance, Avinash Kumar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at ht

[gmx-users] Relating acceleration to pressure

Hello all, This is more of a theoretical question than relating to the software. My question is that when we simulate a pressure driven system (that is I am trying to simulate a nanochannel fluid flow using GROMACS) the pressure is being implemented by defining the group of fluid atom

[gmx-users] nstcomm value

nstcomm depending on a given acceleration. Is there any criteria of deciding the above thing. Avinash Kumar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

[gmx-users] Dielectric constant

terms (int) and for all terms an amplitude (real) ; and a phase angle (real) E_x = 1 0.1 0 E-xt = E-y = E-yt = E-z = E-zt = -- Avinash Kumar

[gmx-users] Dielectric constant

? Please help me. -- Avinash Kumar. 4th year undergraduate, ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't

[gmx-users] FENE potential (Finitely extensible Nonlinear elastic model)

) coeff1 = K (energy/distance^2) coeff2 = R0 (distance) -- Avinash Kumar. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please

[gmx-users] Changing LJ potential

Dear All, I need to define the LJ potential in a new way. Could anybody tell me where the LJ potential is calculated in the GROMACS files. -- Avinash Kumar. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org

[gmx-users] Qeury on freezing an atom with negatice co-ordinates

, Avinash Kumar IIT Kharagpur ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests t

[gmx-users] g_rdf problem

e program does nothing further . I checked for the installation of g_rdf and found it to be installed . My simulation was completed and for command like "trjconv" can read all the frames . Then why is "g_rdf" command failing to read all the frames? eagerly waiting for a reply.

[gmx-users] Calculating velocity profile for nanochannel fluid flow

outside standard GROMACS capabilities or you only use the postprocessing commands of GROMACS . Avinash Kumar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] HELP REGARDING COMMAND g_pvd

Hello all, I saw a command in the analysis part of manual in section 8.14 . The command name is g_pvd . It says it can calculate properties like density of particles per unit volume but I donot find it in the manual nor in my GROMACS installation. Can anybody help me on this? Avinash