Re: [gmx-users] Lysozyme in Water at different pH and Ionic strength

[jkrieger]

I notice that both papers mention modifications to GROMACS and cite the
following:
http://www.ncbi.nlm.nih.gov/pubmed/16471903

> Following up on Justin's reply I just want to add that, not only is it
> possible, as it has been done before. For instance:
>
> http://www.ncbi.nlm.nih.gov/pubmed/18214978
> http://www.ncbi.nlm.nih.gov/pubmed/22072522
>
> Luís Filipe
> ITQB-UNL, Portugal
>
> 2013/11/1 Justin Lemkul 
>
>>
>>
>> On 11/1/13 8:39 AM, xiao wrote:
>>
>>> It is impossible. But you can add proton to the acidic amino acid.
>>>
>>>
>> It's certainly not impossible.  There are constant-pH methods that
>> exist;
>> the list archive contains many posts on this topic, and more information
>> can be found at:
>>
>> http://www.gromacs.org/**Documentation/How-tos/**Constant_pH_Simulation
>>
>> Whether or not you can easily accomplish such simulations in Gromacs is
>> another matter.
>>
>> Standard MD does not allow for dynamic protonation states, so the
>> closest
>> you can get without running more advanced MD is to use fixed protonation
>> states, assigned by pdb2gmx, that are indicative of the most prevalent
>> state of the residues at a given pH value.
>>
>> Changing ionic strength is trivial; that's what genion -conc is for.
>>
>> -Justin
>>
>>
>>
>>>
>>>
>>>
>>> At 2013-11-01 20:36:41,Mass  wrote:
>>>
 Dear Gromacs users,
 Just was wondering if it is possible to protein solution let say
 Lysozyme in Water example of Justin tutorial at different pH and ionic
 strengths, if so how?
 Thanks
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/**mailman/listinfo/gmx-users
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>> --
>> ==**
>>
>> 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
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> --
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Re: [gmx-users] Lysozyme in Water at different pH and Ionic strength

[Luís Carlos Filipe]

Following up on Justin's reply I just want to add that, not only is it
possible, as it has been done before. For instance:

http://www.ncbi.nlm.nih.gov/pubmed/18214978
http://www.ncbi.nlm.nih.gov/pubmed/22072522

Luís Filipe
ITQB-UNL, Portugal

2013/11/1 Justin Lemkul 

>
>
> On 11/1/13 8:39 AM, xiao wrote:
>
>> It is impossible. But you can add proton to the acidic amino acid.
>>
>>
> It's certainly not impossible.  There are constant-pH methods that exist;
> the list archive contains many posts on this topic, and more information
> can be found at:
>
> http://www.gromacs.org/**Documentation/How-tos/**Constant_pH_Simulation
>
> Whether or not you can easily accomplish such simulations in Gromacs is
> another matter.
>
> Standard MD does not allow for dynamic protonation states, so the closest
> you can get without running more advanced MD is to use fixed protonation
> states, assigned by pdb2gmx, that are indicative of the most prevalent
> state of the residues at a given pH value.
>
> Changing ionic strength is trivial; that's what genion -conc is for.
>
> -Justin
>
>
>
>>
>>
>>
>> At 2013-11-01 20:36:41,Mass  wrote:
>>
>>> Dear Gromacs users,
>>> Just was wondering if it is possible to protein solution let say
>>> Lysozyme in Water example of Justin tutorial at different pH and ionic
>>> strengths, if so how?
>>> Thanks
>>> --
>>> 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!
>>> * Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> * Can't post? Read 
>>> http://www.gromacs.org/**Support/Mailing_Lists
>>>
>>>
>>>
> --
> ==**
>
> 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!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
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Re: [gmx-users] Lysozyme in Water at different pH and Ionic strength

[Justin Lemkul]

On 11/1/13 8:39 AM, xiao wrote:

It is impossible. But you can add proton to the acidic amino acid.



It's certainly not impossible.  There are constant-pH methods that exist; the 
list archive contains many posts on this topic, and more information can be 
found at:


http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation

Whether or not you can easily accomplish such simulations in Gromacs is another 
matter.


Standard MD does not allow for dynamic protonation states, so the closest you 
can get without running more advanced MD is to use fixed protonation states, 
assigned by pdb2gmx, that are indicative of the most prevalent state of the 
residues at a given pH value.


Changing ionic strength is trivial; that's what genion -conc is for.

-Justin






At 2013-11-01 20:36:41,Mass  wrote:

Dear Gromacs users,
Just was wondering if it is possible to protein solution let say Lysozyme in 
Water example of Justin tutorial at different pH and ionic strengths, if so how?
Thanks
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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--
==

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] Lysozyme in Water at different pH and Ionic strength

[xiao]

It is impossible. But you can add proton to the acidic amino acid.





At 2013-11-01 20:36:41,Mass  wrote:
>Dear Gromacs users,
>Just was wondering if it is possible to protein solution let say Lysozyme in 
>Water example of Justin tutorial at different pH and ionic strengths, if so 
>how?
>Thanks
>-- 
>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/Search before posting!
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-- 
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[gmx-users] Lysozyme in Water at different pH and Ionic strength

[Mass]

Dear Gromacs users,
Just was wondering if it is possible to protein solution let say Lysozyme in 
Water example of Justin tutorial at different pH and ionic strengths, if so how?
Thanks
-- 
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
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