Re: [gmx-users] Entering ions

[Mohsen Ramezanpour]

sure, thank you.


On Mon, Oct 21, 2013 at 4:49 PM, Justin Lemkul  wrote:

>
>
> On 10/21/13 8:54 AM, Mohsen Ramezanpour wrote:
>
>> Dear Dr. Justin
>>
>> Thank you for your reply
>>
>> You are right, I am sorry for my mistake. I meant Phosphate and Sulfate
>> ions.
>>
>> I want to have these ions in my solution.
>>
>>
> Many force fields include these ions or closely related model compounds.
>  Have a look in the .rtp entries and search the literature.
>
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  |
> (410) 706-7441
>
> ==**
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Re: [gmx-users] Entering ions

[Justin Lemkul]

On 10/21/13 8:54 AM, Mohsen Ramezanpour wrote:

Dear Dr. Justin

Thank you for your reply

You are right, I am sorry for my mistake. I meant Phosphate and Sulfate
ions.

I want to have these ions in my solution.



Many force fields include these ions or closely related model compounds.  Have a 
look in the .rtp entries and search the literature.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Entering ions

[Mohsen Ramezanpour]

Dear Dr. Justin

Thank you for your reply

You are right, I am sorry for my mistake. I meant Phosphate and Sulfate
ions.

I want to have these ions in my solution.



On Mon, Oct 21, 2013 at 1:37 PM, Justin Lemkul  wrote:

>
>
> On 10/21/13 4:45 AM, Mohsen Ramezanpour wrote:
>
>> Dear users
>>
>> I want to use some ions in my simulation (Phosphorus, Sulfur and ...).
>>
>> How can I know in which FF these are present?
>>
>
> Phosphorus and sulfur aren't ions.  There are P and S atomtypes in most
> force fields that are suitable for several types of functional groups, but
> I suspect your description simply isn't accurate enough to begin to guess.
>
>
>  And what can I do if no FF include the interested Ions?
>>
>>
> The answer to this question is always the same - derive them in a manner
> consistent with a force field you have reason to believe will be adequate
> for simulating the species of interest.
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  |
> (410) 706-7441
>
> ==**
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
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Re: [gmx-users] Entering ions

[Justin Lemkul]

On 10/21/13 4:45 AM, Mohsen Ramezanpour wrote:

Dear users

I want to use some ions in my simulation (Phosphorus, Sulfur and ...).

How can I know in which FF these are present?


Phosphorus and sulfur aren't ions.  There are P and S atomtypes in most force 
fields that are suitable for several types of functional groups, but I suspect 
your description simply isn't accurate enough to begin to guess.



And what can I do if no FF include the interested Ions?



The answer to this question is always the same - derive them in a manner 
consistent with a force field you have reason to believe will be adequate for 
simulating the species of interest.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Entering ions

[Mohsen Ramezanpour]

Dear users

I want to use some ions in my simulation (Phosphorus, Sulfur and ...).

How can I know in which FF these are present?
And what can I do if no FF include the interested Ions?

any suggestion is appreciated in advacne
Best
Mohsen
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