[gmx-users] Re: gmx-users digest, Vol 1 #937 - 8 msgs
tccf at epq.ime.eb.br
Mon Aug 18 14:59:01 CEST 2003
I am afraid I didn't understood properly the LD. My system runs well
the EM but how could I perform a PR LD if LD is done only in vacuum ????
I am trying to change tmeperature and friction coefficient values
but it didn't workout yet. My substrates are jump out the box.
Thanks a lot.
IME - Rio de Janeiro - Brazil
> Tanos wrote:
>>> Hi Folks,
>>> I am trying to perform a LD in a protein with 608 residues but the
>>> energy is raising too much and the system is halting. I am not sure of
>>> using the correct procedure. Could someone send me right sequence of
>>> comands to prepare a system to a LD dynamics ?????
> Generally, it would be similar to MD setup procedures, like EM and
> position restrained (PR) equilibration. Does your system minimize well
> in EM? Can you run a short bit of PR MD, or PR LD? The behaviour of LD
> depends on the LD temperature and the friction coefficient. If you
> have the friction wrong, your timescale is off and you might have an
> effective timestep that is too large.
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