[gmx-users] Question about "nsttcouple"

Dear All, We are doing a simulation for ice melting in Efield with thermostat, and we would like to control the frequency for coupling the temperature by setting "nsttcouple". But we always received a warning said it was a unknown parameter during "grompp" in GROMACS V4.0.7 on LINUX. I also tri

[gmx-users] Re: Re: Question about "nsttcouple"

Dear Mark, Thank you for your quick reply. I mean if there is any way we can control the frequency for coupling the temperature if we still use GROMACS V4.0.7 on LINUX? Many thanks, Alex On Jan 17, 2012, at 1:08 AM, gmx-users-requ...@gromacs.org wrote: > On 17/01/2012 7:53 PM, Size Zh

[gmx-users] Question about Andersen thermostat

Dear All, We are doing a simulation for ice melting in Efield with thermostat. We would like use Andersen thermostat to couple the temperature but found that it is not implemented yet, even on the latest version of GROMACS. Is there any way we can employ Andersen thermostat directly on GROMACS

[gmx-users] Parallel Computation of g_rdf

Dear All, I plan to use g_rdf to analyze my system which has thousands of molecules and > 1ms total simulation time. I tried this command on a small system first and found it was very time-consuming. I am just wondering if g_rdf can be executed parallel using MPI? Many thanks, Size Zh

[gmx-users] Dielectric Constants

2e+03 6.991e-01 - I also tried to use g_dielectric command, but never succeeded, and always got a message: Fatal error: nparm = 0 in file expfit.c, line 465 Is there any way that can obtain the average dielectric constants of the whole simulation? Or did I do

[gmx-users] Total Kinetic Energy And Rotational And Translational Kinetic Energy

, i.e. the total KE and the sum of rotational KE and translational KE was not the same, and actually their gap was kind of large. I totally have no idea about this. Is there something wrong or something I missed? Many thanks, Size Zheng-- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Problem of Kinetic Energy

-ekr. Even though I normalize the total kinetic energy (reported from g_energy) with molecular number, its value is still not equal to the sum of the rotational and translational kinetic energy ,obtained from g_traj with options of -ekt and -ekr. Many thanks, Size Zheng-- gmx-users mailing list

[gmx-users] Re: Problem of Kinetic Energy

= 1.71635114e-03, c12= 4.54480232e-06 >>>>> c6= 2.60732602e-03, c12= 6.42257237e-06 >>>>> c6= 3.75109637e-04, c12= 2.77185705e-07 >>>>> c6= 1.98187144e-03, c12= 5.24788538e-06 >>>>> c6= 6.18919948e-05, c12= 7.54611396e-09 >>>>> c6

Re: [gmx-users] Problem of Kinetic Energy

Hi Mark, When I used the g_traj with options of -ekt and -ekr, i made a selection as follow Group 0 ( System) has 6400 elements Group 1 (TP4) has 6400 elements Select a group: 1 Selected 1: 'TP4' So according to you that g_traj uses the whole 1600-molecules' COM to

[gmx-users] Kinetic energy of a single molecule

me to produce the total kinetic energy of the whole system. For the singe molecule, there were only LJ, Coulomb and T options. Is there any method to generate the kinetic energy just for the single molecule? Many thanks, Size Zheng-- gmx-users mailing listgmx-users@gromacs.org