[gmx-users] Calculating Temperature from Velocity

I am trying to calculate the temperature from the final velocity posted in the confout.gro file after a simulation runs. I have implemented a berendsen thermostat to control the temperature to 300K and ran it for 1ns. Looking at g_energy the final temperature of the system is 299.981. Statistics ov

[gmx-users] Re: Calculating Temperature from Velocity

, say 10-12 atoms, the temperature of these atoms varies alot while the temperature the whole system does not, why is this? Is there a way to accurately determine the temperature of a small number of atoms? Thanks again, Andy On Mon, Sep 22, 2008 at 10:42 AM, Andy Shelley <[EMAIL PROTECTED]>

Re: [gmx-users] Calculating Temperature from Velocity

Jochen, I am confused on how to calculate the bond length constraints. I notice after I run grompp it gives the output of degrees of freedom: Number of degrees of freedom in T-Coupling group TOP is 59.97 Number of degrees of freedom in T-Coupling group BOTTOM is 59.97 Number of degrees of freedo

[gmx-users] Heat Flux and Lambda

I have been reading through the mailing list and have read some discussion that heat flux can be indicated by the value of lambda. Can I calculate the amount of heat flux from the lambda value? Thanks, Andy Shelley ___ gmx-users mailing listgmx

Re: [gmx-users] Heat Flux and Lambda

in md.log file. > > Thanks, > Andy Shelley > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/g

[gmx-users] Setting constant velocity

Is there a way to set a constant velocity to simulate fluid flow? I know I can apply a force to increase velocity, but can I keep the velocity constant after that? Thanks, Andy ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/ma

Re: [gmx-users] atoms not part of any of the T-coupling groups

Garry, I believe you are trying to not temperature couple the 4 zincs. To do this put the 4 zincs in one group and include that group in the listing of tc_grps and then correspondingly assign tau_t. tau_t=0 means no temperature coupling, but I think you will also need to give a temperature for the

[gmx-users] Using pull code to simulate slab flow

I am trying to simulate slab flow 5 m/s in the x direction using the afm pull code. I use the following parameters in the pull.ppa file with full periodic boundary conditions. verbose = no runtype = afm ngroups = 1 group_1 = water reference_group = weights_1 = reference_weights = reftype = com_t0

[gmx-users] Heat Flux on CNT

Hello, I am trying to model heat flux across a carbon nanotube and was planning on using the annealing function to set and hold a temperature difference across the tube to create a heat flux. I was wondering if anyone had some thoughts on short comings with this idea or a better way to model the

[gmx-users] Nitrogen Flow over cylinder

assigning a linear velocity profile to the Nitrogen. I realize this will probably have to be done in NEMD. Any thoughts or ideas would be appreciated. Andy Shelley ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx

RE:[gmx-users] cannot print velocity information to trr/xtc files (Carbon Nanotube inside water)

I am to accelerate water while freezing another group and would like to know velocity information as has been posted before and was wondering if a solution to the problem has been found. Andy Nadir Kaplan wrote: >>> What is going on here? How can I get velocity info? Any help will be >>> greatly

[gmx-users] Determining temperature from velocities

I was wondering how g_energy determines the temperature of the groups. I am trying to measure temperature based upon distance from a point radially outward. To implement I thought about writing a code to input the final velocities to determine average temperature based upon a central point. Thanks

[gmx-users] simulating with air

I would like to use air as a "solvent" with genbox instead of water. I have read the manual but have not found any information to help me. Any information would be beneficial. Thanks, Andy ___ gmx-users mailing listgmx-users@gromacs.org http://www.gr

[gmx-users] Force Field Parameters Nitrogen and Oxygen

I am trying to simulate air and have not been able to find force field parameters for a Nitrogen Nitrogen bond or Oxygen Oxygen bond. If you could please direct me to where these could be found I would appreciate it. Thanks, Andy ___ gmx-users mailing l

[gmx-users] Re: simulating with air

k if you use LJ-12-6 parameters they > would appear close enough both in the gromacs FF and anywhere else. > > Pls. let me know if you need further help or guide. > > Best, > Vitaly > > > 2008/8/13 Andy Shelley <[EMAIL PROTECTED]>: > > Vitaly, > > > &

[gmx-users] Re: simulating with air

I am currently just trying to get 1 molecule to work. So I added the morse potential to ffgmxbon.itp as: [ bondtypes ] ; ij funcb0 kb NN3 0.10980 943.04330.2642 and received this error message after using x2top with an ENCAD force field Fatal error: N

[gmx-users] Using Morse potentials with ENCAD force field

I have added a mixture of oxgen and nitrogen to a simulation with a cnt. The oxygen and nitrogen use morse potentials and the cnt uses the encad force field. Previously I simulated the cnt with the default water and it worked well. When using my "air" mixture the cnt collapses even if a small numb

Re: [gmx-users] Using Morse potentials with ENCAD force field

Actually I think I am using the gromos force field. I have been using Christopher Stiles page as a guide to get started with using CNT http://cs86.com/CNSE/SWNT.htm. I realize now that all the modifications were made to ffgmx files. So I believe I am using the gromos forcefield. Is the forcefield

[gmx-users] Re: Using Morse potentials with ENCAD force field

not be equalizing out to an even distribution of oxygen by nitrogen? Andy It seems because your box should be a bit longer to succeed. Try to enlarge the side (13.2 nm) length. 2008/8/21 Andy Shelley <[EMAIL PROTECTED]>: > No problem the term flattens is porbably not the best

[gmx-users] Re: Re[2]: Using Morse potentials with ENCAD force field

I have been able to get the molecules to become more homogenous. The problem was I wasn't running the system long enough. I looked at the energy of the system though and am getting very large fluctuations. The system was ran with the initial temperature set at 300K by setting inital velocities, bu

[gmx-users] Re: Re[4]: Using Morse potentials with ENCAD force field

2, 2008 at 10:00 AM, Vitaly Chaban < > [EMAIL PROTECTED]> wrote: > > AS> > > AS> You have problems with your force field. > > AS> > > AS> If you send me all the files describing your system I'll try to see > > AS> what really happens when

[gmx-users] Re: Re[6]: Using Morse potentials with ENCAD force field

I am trying to make a radial temperature profile of a given thickness. I originally used the confout.gro file containing the final output of velocity and position of each atom to calculate the temperature from the velocity but would like to take time averages now. Andy On Sat, Sep 6, 2008 at 4:21