Yeah... A equilibration can be complish within the ps n we have to make
ensure that the there should not be more fluctuation in the potential energy
in other words it should be stabilize.
On 5 October 2010 17:47, Justin A. Lemkul wrote:
>
>
> Anil Mhashal wrote:
>
>> Just plot a graph of the pot
- Original Message -
From: Anil Mhashal
Date: Tuesday, October 5, 2010 23:11
Subject: Re: [gmx-users] Reg:Equilibration
To: Discussion list for GROMACS users
> Just plot a graph of the potential energy with respect to the time and check
> the energy fluctuation, it should b
Anil Mhashal wrote:
Just plot a graph of the potential energy with respect to the time and
check the energy fluctuation, it should be less than 10% of the average
potential energy then u can say that ur protein is equilibrated.
I would think that, for most systems, a fluctuation of 10% is
Just plot a graph of the potential energy with respect to the time and check
the energy fluctuation, it should be less than 10% of the average potential
energy then u can say that ur protein is equilibrated.
On 5 October 2010 17:16, vinothkumar mohanakrishnan wrote:
> hi anil
>
> i get the pote
hi anil
i get the potential energy at the end of the mdrun. if i want to calulate
the deviation with what i should compare and calculate the deviation.can you
be more specific.
Regards
Vinoth
On Tue, Oct 5, 2010 at 4:51 PM, Anil Mhashal wrote:
> To check ur equilibration, just look at the pote
To check ur equilibration, just look at the potential energy and find out
the deviation in the energy if the deviation in the energy is within 10%
then ur equilibration is successful...
On 5 October 2010 14:56, vinothkumar mohanakrishnan wrote:
> Hi all
>
> Suppose say i have a box of decane mol
vinothkumar mohanakrishnan wrote:
Hi all
Suppose say i have a box of decane molecules and i want to equilibrate.
say i have all the necessary files to run mdrun. on what basis i say
whether my equilibration is successful r not after the mdrun. what
properties i should measure to know whethe
Hi all
Suppose say i have a box of decane molecules and i want to equilibrate. say
i have all the necessary files to run mdrun. on what basis i say whether my
equilibration is successful r not after the mdrun. what properties i should
measure to know whether my equilibration was successful.
Regar
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