I have tried so many times but the temperature increases and neither is the energy constant. :(
-
karamyog. :(
On 5/19/06, karamyog singh <[EMAIL PROTECTED]> wrote:
I guess since after the first run, the forces between atoms is not zero(only negligible), when i do the 2nd run, the atoms start moving under the action of these forces and since there is no temperature scaling or pressure scaling, we can or might see an increase in KE as in my case. So an increase might be correct.
Am I right? Please answer this because I am an undergraduate student and this will clear my misconception, if any. :)
Thanks in advance.
-Karamyog.On 5/18/06, Mark Abraham < [EMAIL PROTECTED]> wrote:karamyog singh wrote:
> Well, I am back. Remember my first and second mdruns. In my second,
> after stablizing my initial configuration in the 1st md run, I used cut
> off upto 6.3 whereas the potential minima is at 0.309. 6.3 is quite
> large a distance compared to 0.309. In the second run, the kinetic
> energy increases which is correct but the total energy doesnt seem to
> remain constant even when there are 3 million steps involved.
Why is increasing KE correct?
> How is this constant energy mode? KE increases(accepted) but the total
> never seems to be constant. I cant keep increasing my no. of steps.
> moreover how can so many vibrations be introduced at a temp. of 0.001 K.
It's well known (as I said a few emails ago) that cut-offs in NVE will
cause system heating - that's why people tend to use NVT if they are
using cut-offs. Expected NVE behaviour for this sort of system as a
function of cut-off is outside my experience, but you can use g_energy
to judge how fast KE and thus total energy is increasing as a function
of simulation time. If that rate varies with the cutoff, then I'd say
there's the problem.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED] .
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
