Re: [gmx-users] GPCR MD Tutorial Using GROMACS (URL)

[Anirban Ghosh]

Hello Albert,

On our cluster I usually get around 25-30 ns/day running on 120 cores
(system size around 85K atoms) with PME.

Regards,

Anirban

On Thu, Apr 26, 2012 at 5:28 PM, Albert  wrote:

> Hi Anirban:
>   how many ns/day for your simulations? Did you use PME?
>
> best
> Albert
>
>
>
> On 04/26/2012 12:59 PM, Anirban Ghosh wrote:
>
>> Hello Albert,
>>
>> Good to know that!
>> I have carried out simulations using this FF in the range of 600 ns.
>>
>> Regards,
>>
>> Anirban
>>
>
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Re: [gmx-users] GPCR MD Tutorial Using GROMACS (URL)

[Albert]

Hi Anirban:
   how many ns/day for your simulations? Did you use PME?

best
Albert


On 04/26/2012 12:59 PM, Anirban Ghosh wrote:

Hello Albert,

Good to know that!
I have carried out simulations using this FF in the range of 600 ns.

Regards,

Anirban


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Re: [gmx-users] GPCR MD Tutorial Using GROMACS (URL)

[Anirban Ghosh]

Hello Albert,

Good to know that!
I have carried out simulations using this FF in the range of 600 ns.

Regards,

Anirban

On Thu, Apr 26, 2012 at 3:47 PM, Albert  wrote:

> Hello Anirban:
>
>  thanks for kind comments.
>  How long did you mean " fairly long simulation time" ? does 1u ns belongs
> to this range? CHARMM36 ff is available in gromacs website and we can
> download it and put them into top directory and then it works. It is not
> need to make any modification by ourselves.
>
> best
> Albert
>
>
>
> On 04/26/2012 11:53 AM, Anirban Ghosh wrote:
>
>> Hello Albert,
>>
>> Thanks.
>> Yes, CHARMM36 indeed handles lipids very well. But currently GROMACS
>> 4.5.5 provides only the option for CHARMM27 FF and I found that ff43a1 very
>> well preserves the characters of both the protein as well as the lipids for
>> fairly long simulation time, hence I used that FF in the tutorial. But one
>> can surely add CHARMM36 to GROAMCS by doing all the necessary topology
>> conversions.
>>
>>
>> Regards,
>>
>> Anirban
>>
>
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Re: [gmx-users] GPCR MD Tutorial Using GROMACS (URL)

[Albert]

Hello Anirban:

  thanks for kind comments.
  How long did you mean " fairly long simulation time" ? does 1u ns 
belongs to this range? CHARMM36 ff is available in gromacs website and 
we can download it and put them into top directory and then it works. It 
is not need to make any modification by ourselves.


best
Albert


On 04/26/2012 11:53 AM, Anirban Ghosh wrote:

Hello Albert,

Thanks.
Yes, CHARMM36 indeed handles lipids very well. But currently GROMACS 
4.5.5 provides only the option for CHARMM27 FF and I found that ff43a1 
very well preserves the characters of both the protein as well as the 
lipids for fairly long simulation time, hence I used that FF in the 
tutorial. But one can surely add CHARMM36 to GROAMCS by doing all the 
necessary topology conversions.



Regards,

Anirban


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Re: [gmx-users] GPCR MD Tutorial Using GROMACS (URL)

[Anirban Ghosh]

Hello Albert,

Thanks.
Yes, CHARMM36 indeed handles lipids very well. But currently GROMACS 4.5.5
provides only the option for CHARMM27 FF and I found that ff43a1 very well
preserves the characters of both the protein as well as the lipids for
fairly long simulation time, hence I used that FF in the tutorial. But one
can surely add CHARMM36 to GROAMCS by doing all the necessary topology
conversions.


Regards,

Anirban

On Thu, Apr 26, 2012 at 3:08 PM, Albert  wrote:

>  it seesm to be good.
> just one pieces of advices, why not use CHARMM36 for this tutorial ? since
> it is the best FF for lipids currently.
>
>
> On 04/26/2012 11:14 AM, Anirban Ghosh wrote:
>
> Hi ALL,
>
>  I have prepared a step-wise tutorial for running a MD simulation of a
> GPCR protein inserted in a lipid bilayer. It can be found at the following
> URL:
>
>  https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial
>
>  I sincerely hope it will help people who are new to such simulations and
> the GROMACS community in general. This tutorial is adapted from the
> membrane protein tutorial prepared by Justin Lemkul.
>
>
>  Regards,
>
>  Anirban
>
>
>
>
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Re: [gmx-users] GPCR MD Tutorial Using GROMACS (URL)

[Albert]

it seesm to be good.
just one pieces of advices, why not use CHARMM36 for this tutorial ? 
since it is the best FF for lipids currently.


On 04/26/2012 11:14 AM, Anirban Ghosh wrote:

Hi ALL,

I have prepared a step-wise tutorial for running a MD simulation of a 
GPCR protein inserted in a lipid bilayer. It can be found at the 
following URL:


https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial

I sincerely hope it will help people who are new to such simulations 
and the GROMACS community in general. This tutorial is adapted from 
the membrane protein tutorial prepared by Justin Lemkul.



Regards,

Anirban




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