Re: [gmx-users] Turning off electrostatic or Van der Waals interactions

2009-02-24 Thread Lee Soin 
Thanks!

2009/2/24 Berk Hess 

> Hi,
>
> Setting
> epsilon_r = 0
> in your mdp file will turn off all electrostatics.
> If you are concerned about efficiency, you should set all charges
> in your topology to zero.
>
> Berk
>
> --
> Date: Tue, 24 Feb 2009 09:49:25 +0200
> Subject: Re: [gmx-users] Turning off electrostatic or Van der Waals
> interactions
> From: omer...@gmail.com
> To: gmx-users@gromacs.org
>
>
>  Why not create "dummy" topologies, without charges/vdw ?
> Another option, which I am not sure of its effect, is, perhaps, to take
> extremely small cutoffs.
> --Omer.
>
>
> Lee Soin wrote:
>
> I'm trying to rule out the effect of electrostatic or Van der Waals
> interactions while performing a simulation. Do you mean that I should modify
> the code and re-compile?
>
>
>
> --
> What can you do with the new Windows Live? Find 
> out<http://www.microsoft.com/windows/windowslive/default.aspx>
>
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>



-- 
Sun Li
Department of Physics
Nanjing University, China
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RE: [gmx-users] Turning off electrostatic or Van der Waals interactions

2009-02-24 Thread Berk Hess 

Hi,

Setting
epsilon_r = 0
in your mdp file will turn off all electrostatics.
If you are concerned about efficiency, you should set all charges
in your topology to zero.

Berk

Date: Tue, 24 Feb 2009 09:49:25 +0200
Subject: Re: [gmx-users] Turning off electrostatic or Van der Waals 
interactions
From: omer...@gmail.com
To: gmx-users@gromacs.org

Why not create "dummy" topologies, without charges/vdw ?
Another option, which I am not sure of its effect, is, perhaps, to take 
extremely small cutoffs.
--Omer.

 Lee Soin wrote:


I'm trying to rule out the effect of electrostatic or Van der Waals 
interactions while performing a simulation. Do you mean that I should modify 
the code and re-compile?






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Re: [gmx-users] Turning off electrostatic or Van der Waals interactions

2009-02-23 Thread Omer Markovitch 
Why not create "dummy" topologies, without charges/vdw ?
Another option, which I am not sure of its effect, is, perhaps, to take
extremely small cutoffs.
--Omer.


> Lee Soin wrote:
>
>> I'm trying to rule out the effect of electrostatic or Van der Waals
>> interactions while performing a simulation. Do you mean that I should modify
>> the code and re-compile?
>>
>>
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Re: [gmx-users] Turning off electrostatic or Van der Waals interactions

2009-02-23 Thread Justin A. Lemkul 



Lee Soin wrote:
I'm trying to rule out the effect of electrostatic or Van der Waals 
interactions while performing a simulation. Do you mean that I should 
modify the code and re-compile?




No, I mean use the free energy options in the .mdp file.  You may be able to use 
a B-state in the topology with dummy atoms to accomplish what you want to do.


-Justin


2009/2/23 Justin A. Lemkul mailto:jalem...@vt.edu>>



Lee Soin wrote:

Hi!
Is there an option to turn off electrostatic or Van der Waals
interactions in GROMACS?


Look into the free energy code; if this is not your intent, be more
specific with what you are trying to do.

-Justin

-- 
Sun Li

Department of Physics
Nanjing University, China




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-- 



Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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--
Sun Li
Department of Physics
Nanjing University, China


--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Turning off electrostatic or Van der Waals interactions

2009-02-23 Thread Lee Soin 
I'm trying to rule out the effect of electrostatic or Van der Waals
interactions while performing a simulation. Do you mean that I should modify
the code and re-compile?

2009/2/23 Justin A. Lemkul 

>
>
> Lee Soin wrote:
>
>> Hi!
>> Is there an option to turn off electrostatic or Van der Waals interactions
>> in GROMACS?
>>
>>
> Look into the free energy code; if this is not your intent, be more
> specific with what you are trying to do.
>
> -Justin
>
>  --
>> Sun Li
>> Department of Physics
>> Nanjing University, China
>>
>>
>> 
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
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>>
>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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>



-- 
Sun Li
Department of Physics
Nanjing University, China
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Re: [gmx-users] Turning off electrostatic or Van der Waals interactions

2009-02-23 Thread Justin A. Lemkul 



Lee Soin wrote:

Hi!
Is there an option to turn off electrostatic or Van der Waals 
interactions in GROMACS?




Look into the free energy code; if this is not your intent, be more specific 
with what you are trying to do.


-Justin


--
Sun Li
Department of Physics
Nanjing University, China




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--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Turning off electrostatic or Van der Waals interactions

2009-02-23 Thread Lee Soin 
Hi!
Is there an option to turn off electrostatic or Van der Waals interactions
in GROMACS?

-- 
Sun Li
Department of Physics
Nanjing University, China
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