Ok Thanks.
On Tue, Oct 18, 2011 at 4:41 PM, Justin A. Lemkul wrote:
>
>
> Kavyashree M wrote:
>
>> Hello,
>>
>> Thank you. I got the point but I have a doubt,
>> "equilibrate under NPT until the pressure and
>> temperature are stable, then switch to NVT to
>> eliminate the boiling issue", how ex
Kavyashree M wrote:
Hello,
Thank you. I got the point but I have a doubt,
"equilibrate under NPT until the pressure and
temperature are stable, then switch to NVT to
eliminate the boiling issue", how exactly it will
eliminate the boiling issue if we dont use higher
pressure while equlibrating?
Hello,
Thank you. I got the point but I have a doubt,
"equilibrate under NPT until the pressure and
temperature are stable, then switch to NVT to
eliminate the boiling issue", how exactly it will
eliminate the boiling issue if we dont use higher
pressure while equlibrating? (as you said that
it is
Kavyashree M wrote:
Ok, The protein I am going to simulate is from a hyperthermophilic organism
which lives in deep oceanic thermal vents. so in the deep vents the pressure
will be enormous. even though I do not have much information about the
magnitude of pressure in that site and inside the c
Ok, The protein I am going to simulate is from a hyperthermophilic organism
which lives in deep oceanic thermal vents. so in the deep vents the pressure
will be enormous. even though I do not have much information about the
magnitude of pressure in that site and inside the cell of that organism.. I
Kavyashree M wrote:
Hello,
I am sorry those were two different questions.. I wanted to know what
this statement actually mean?
"The set pressure should reflect whatever system you are trying to model."
You haven't fully explained what exactly you're trying to do yet, so I'm taking
a stab
Hello,
I am sorry those were two different questions.. I wanted to know what
this statement actually mean?
"The set pressure should reflect whatever system you are trying to model."
Thank you
With Regards
Kavya
>
> I don't see the connection to my comment about pressure, but I'll address
> this
Hello,
Yes, I have come across that but If the temperature is below
the boiling point its fine. But if it crosses the boiling temperature
in order keep the water as liquid isnt it necessary to increase the
pressure. I understand that the water models do not exactly predict
the transition temperatu
Kavyashree M wrote:
Hello,
The set pressure should reflect whatever system you are trying to model.
This statement is not very clear to me.. But when the mdout.mdp file
after grompp
during energy minimization is examined it says -
gen-vel = no
gen-temp
Hello,
The set pressure should reflect whatever system you are trying to model.
>
This statement is not very clear to me.. But when the mdout.mdp file after
grompp
during energy minimization is examined it says -
gen-vel = no
gen-temp = 300
gen-seed
On 17/10/2011 10:58 PM, bipin singh wrote:
I have not understood what you mean by
"Energy minimization is (theoretically) at 0 K, as there are no velocities
and it is not a true dynamical process."
It is clear to me that at 0K there would be no velocities but then why
during minimization we expec
In the energy minimisation step, any "conformational rearrangement" taking
place is not a function of time, it is just an algorithm for reaching a
basin of minimum energy:
(http://www.gromacs.org/Documentation/Terminology/Energy_Minimisation),
hence there are not velocities in the atoms of the sy
I have not understood what you mean by
"Energy minimization is (theoretically) at 0 K, as there are no velocities
and it is not a true dynamical process."
It is clear to me that at 0K there would be no velocities but then why
during minimization we expect
some conformational rearrangement of side c
Well,as I found in literatures people have used same( 1 atm) pressure
at high temperature simulations(NPT simulations).
with different water models.As most of the force field parameters are
determined generally at 300K and 1 atm.
What would be the the possible drawbacks of using the same pressure(o
Kavyashree M wrote:
Thank you,
What about the pressure that need to be used at that temperature
(for a system of a protein in tip4p water)
The set pressure should reflect whatever system you are trying to model.
-Justin
Thank you
With Regards
Kavya
On Mon, Oct 17, 2011 at 3:29 PM, bipin
bipin singh wrote:
As far as I know we do energy minimization at room temperature only.
Energy minimization is (theoretically) at 0 K, as there are no velocities and it
is not a true dynamical process.
Only during equilibration
(NVT and NPT) we use high temperature for maintaining proper
Thank you,
What about the pressure that need to be used at that temperature
(for a system of a protein in tip4p water)
Thank you
With Regards
Kavya
On Mon, Oct 17, 2011 at 3:29 PM, bipin singh wrote:
> As far as I know we do energy minimization at room temperature only.
> Only during equilibra
As far as I know we do energy minimization at room temperature only.
Only during equilibration
(NVT and NPT) we use high temperature for maintaining proper density
before starting the final production run.
On Mon, Oct 17, 2011 at 15:15, Kavyashree M wrote:
> Dear users,
>
> For simulating a prote
Dear users,
For simulating a protein at high temperature (more than 300K,
less than 400K) using OPLSAA forcefield, what are the parameters
other than Temperature that need to be taken care of?
Does the energy minimization step also needs to be done at high
temperature? (here my aim is not to simul
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