[gmx-users] Re: gmx-users digest, Vol 1 #937 - 8 msgs

[Tanos]

    Dear Anton,
    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.
    Tanos Franca
    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.
>