[gmx-users] Re: Possible bug in the temperature calculation from rerun

Bastien Loubet bastien at memphys.sdu.dk
Tue Oct 2 13:04:42 CEST 2012

Dear gmxusers,

Thank you for your answers so far. I have run a few more test rerun and here
is what I got:
  -The number of degree of freedom are the same whatever the topology I run
with, both in the log file and from the grompp output.
  -Comparing the trajectories created from rerun with gmxdump and diff show
only minor differences, such as atoms positioned on one side or the other of
the simulation box. The velocities are strictly the same however. Here is an

<       x[394728]={ 1.32183e+02,  3.15341e+00,  5.17869e+00}
<       x[394729]={ 1.32054e+02,  3.10839e+00,  5.14599e+00}
<       x[394730]={ 1.32314e+02,  3.17612e+00,  5.13366e+00}
>       x[394728]={-7.17163e-04,  3.15341e+00,  5.17869e+00}
>       x[394729]={-1.29196e-01,  3.10839e+00,  5.14599e+00}
>       x[394730]={ 1.29883e-01,  3.17612e+00,  5.13366e+00}

  -If I use another topology where I only have the interaction with water
not set to zero (still with electrostatic), I get a temperature of ~326K
intermediate between the desired value of 325K and the value I got with all
the interaction shutdown of ~327K.
  -Turning the temperature/pressure coupling on or off do not change the
I think there is a problem in the calculation of the kinetic energy that
translate to the temperature. However setting all the interaction but the
electrostatic to zero should not modify the kinetic energy calculated from
'mdrun -rerun'.
I do not know how to proceed from here, maybe I should post my mdp top and
log files here or on the developers forum ?

Have a good day,

Bastien Loubet

View this message in context: http://gromacs.5086.n6.nabble.com/Possible-bug-in-the-temperature-calculation-from-rerun-tp5001194p5001508.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

More information about the gromacs.org_gmx-users mailing list