[gmx-users] Re: Simulation in the high temperature conditions

James Starlight jmsstarlight at gmail.com
Mon Apr 9 08:18:21 CEST 2012

By the way I've completed equilibration phase of my system ( receptor in
Ccl4-water membrane mimicking layer) in the hight temperature conditions. :)

During 3ns I gradually increased temperature from 300 to 700k with posres
applied on the Ccl4 C atoms and all atoms of protein. After this I've
changed posres applied on the protein to the backbone atoms only and
started gradually decrease fc falue ( from 1000 to 250 ). The overal system
was stabile and I've noticed linnear increase of the total energy
accompanied by such increase of temperature.

Than  When I've removed posres from side-chains I've noticed bigger RMSD in
potential energy of my system.

The only artifact that I've noticed is that some water was moved into the
Ccl4 layer during this equilibration. How I could prevent such layer mixing
without applying posres on water? I need free-water in my system because I
want to see how some water move into the receptor that have a chanell wich
some internal- water cavities having functional meaning.
Does some operation with the COM option could prevent mixing of some
differen solvent layers ?
At the curent moment I've difined COM as

Protein_CCl4 SOL_NA_CL_XW

where XW is the water observed in the X-ray structure of that protein (
I've defined that mollecules in separate layer)

Thanks for help


4 апреля 2012 г. 18:14 пользователь Justin A. Lemkul <jalemkul at vt.edu>написал:

> James Starlight wrote:
>> Justin,
>> 1) I've defined 5 steps for specified definition of the time of each step
>> as well as for more flexibile controle of the such annealing: e.g I want
>> that equilibration step corresponded to the temperature between 320 and
>> 330K will be longer than between first step corresponded to 300-310K etc
> OK, that makes sense.  What you showed before does not do that, hence my
> confusion.
>> 2) About velosities. As I understood for annealing equilibration gen_temp
>> must be equal to the starting temperature of such equilibration ( gen_temp=
>> 300 in the above example). But in what exactly circumstances the changing
>> in gen_temp could be usefull? As I've told after such annealing
>> equilibration I want to simulate my system on the high temperature
>> condition for efficient conformation sampling. Might it be that initial
>> high velocities could be usefull for such sampling efficacy?
> I'm not clear on what you're asking.  If you are generating velocities
> (which you wouldn't after you reach your target via SA or equilibration),
> then you don't need gen_temp or gen_vel.  If you're starting a new run,
> then gen_temp should be equal to the ref_t value you wish to use for the
> simulation.  If your gen_temp and ref_t values are not the same, then it is
> quite possible that the simulation will crash or give very unexpected
> results due to potential instabilities in the thermostat algorithm.
> -Justin
> --
> ==============================**==========
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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