Re: [gmx-users] Simulation of pure water

[Mark Abraham]

Hi,

On Wed, 7 Jun 2017 06:37 G R  wrote:

> Dear all,
>
> I want to calculate the relaxation of pure water cell at room temperature
> and at freezing point, monitoring its equilibration in volume and in
> potential energy. I have 3 question: 1) Can I use packmol for my initial
> configuration?


Maybe, I don't know. gmx solvate works.

if there is any other option,please tell me. 2) Can I use
> easily pdb2gmx to generate the topology file?


Not really, it's designed for solute in water systems. But you can take any
such topology and remove the solute moleculetype and subsections.

3) Which Forcefield is better
> for this calculation?
>

You're not really going to use what is commonly called a force field, but
just a water model. There's lots of them, and you should choose one that
has been shown to be useful for your kind of study. That's the science
part, and your job ;-)

Mark

I'v already read some tutorial, but if you have any suggestion it woulb be
> appreciated.
>
> Thank you in advance
>  GR
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[gmx-users] Simulation of pure water

[G R]

Dear all,

I want to calculate the relaxation of pure water cell at room temperature
and at freezing point, monitoring its equilibration in volume and in
potential energy. I have 3 question: 1) Can I use packmol for my initial
configuration? if there is any other option,please tell me. 2) Can I use
easily pdb2gmx to generate the topology file? 3) Which Forcefield is better
for this calculation?

I'v already read some tutorial, but if you have any suggestion it woulb be
appreciated.

Thank you in advanc
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[gmx-users] Simulation of pure water

[G R]

Dear all,

I want to calculate the relaxation of pure water cell at room temperature
and at freezing point, monitoring its equilibration in volume and in
potential energy. I have 3 question: 1) Can I use packmol for my initial
configuration? if there is any other option,please tell me. 2) Can I use
easily pdb2gmx to generate the topology file? 3) Which Forcefield is better
for this calculation?

I'v already read some tutorial, but if you have any suggestion it woulb be
appreciated.

Thank you in advance
 GR
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