[gmx-users] T-coupling of water and ion

[Jian Zou]

Hi Anton,

I check the manual of g_traj and found that
"Option -ot plots the temperature of each group, provided velocities are 
present in the trajectory file. No corrections are made for constrained 
degrees of freedom! This implies -com."

So, for one water molecule, DOF wil change from 3x3=9 (constaints=no) to 
9-3=6 (constraints=all, 2 bond length and 1 bond angle).

I assume that g_traj calculate the temperature from the kinetic energy, 
using
E_kinetic = 1/2 x N_DOF x kB x T
to get the temperature, where N_DOF is the number of degree of freedom.

I multiply, by a factor of 9/6=1.5, the SOL temperature calculated by 
g_traj, got
####
# time   T_SOL     T_SOL x 1.5
####
   0    263.260     394.89
  20    267.164     400.746
  40    267.071     400.6065
  60    269.949     404.9235
  80    270.667     406.0005
 100    268.766     403.149
 120    269.703     404.5545
 140    270.330     405.495
 160    270.175     405.2625
 180    267.566     401.349
 200    268.778     403.167
 220    267.596     401.385
It seems to be the ref_t I defined for "SOL" tc_group in my mdp.

In the same way, should I get the factor for the "RNA" tc_group, and get the 
"400K" as the ref_t.

Is this correct?


But how about the temperature for sodium cation in my system?
How to explain the large fluctuation in both g_traj result and g_energy 
result?
Do these results imply large heat transfer from Na+ and SOL?


THank you so much for your comment.


Regards,

Jian Zou