Re: [gmx-users] Quick question about pressure coupling

2013-09-11 Thread HANNIBAL LECTER 
Would there be artifacts because of that?


On Wed, Sep 11, 2013 at 9:20 AM, HANNIBAL LECTER  wrote:

> Yes
>
>
> On Wed, Sep 11, 2013 at 9:18 AM, Justin Lemkul  wrote:
>
>>
>>
>> On 9/11/13 9:09 AM, HANNIBAL LECTER wrote:
>>
>>> 500ps simulations. Yes everything is immersed in a bath of water. Can you
>>> please elaborate a little more as to why do you doubt semiisotropic
>>> coupling may not be necessary?
>>>
>>>
>> Water should compress isotropically.  I understand where you're coming
>> from, given that you have observed a seemingly semiisotropic compression of
>> the system, but physically that is not right.  Something like a membrane,
>> that has properties that make it sensible to couple x-y and z compression
>> separately, would use semiisotropic coupling.
>>
>> Is this a system in which you're using freezegrps?
>>
>> -Justin
>>
>>
>>> On Wed, Sep 11, 2013 at 9:05 AM, Justin Lemkul  wrote:
>>>
>>>

 On 9/11/13 9:01 AM, HANNIBAL LECTER wrote:

  I am trying to simulate a peptide inside a nanotube and using isotropic
> pressure coupling for the system. The nanotube is immersed in a
> cuboidal
> box of water and aligned along the z direction of the box.
>
> The XX, YY components of the stress tensor are about ~570 bars and the
> ZZ
> component is about -1179 yielding a total pressure of about 2 bars
> whereas
> my set pressure is ~1.01325 bars. Is this okay or should I be using
> semiisotropic coupling?
>
>
>  Over how long a time period are these values?  If everything is
 immersed
 in a bath of water, I doubt semiisotropic coupling is necessary.

 -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 >>> umaryland.edu > | (410)
 706-7441

 ==

 --
 gmx-users mailing listgmx-users@gromacs.org
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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
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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Re: [gmx-users] Quick question about pressure coupling

2013-09-11 Thread Justin Lemkul 



On 9/11/13 9:20 AM, HANNIBAL LECTER wrote:

Yes



Then I would call your outcome an artifact of a physically unreasonable setup.

-Justin



On Wed, Sep 11, 2013 at 9:18 AM, Justin Lemkul  wrote:




On 9/11/13 9:09 AM, HANNIBAL LECTER wrote:


500ps simulations. Yes everything is immersed in a bath of water. Can you
please elaborate a little more as to why do you doubt semiisotropic
coupling may not be necessary?



Water should compress isotropically.  I understand where you're coming
from, given that you have observed a seemingly semiisotropic compression of
the system, but physically that is not right.  Something like a membrane,
that has properties that make it sensible to couple x-y and z compression
separately, would use semiisotropic coupling.

Is this a system in which you're using freezegrps?

-Justin



On Wed, Sep 11, 2013 at 9:05 AM, Justin Lemkul  wrote:




On 9/11/13 9:01 AM, HANNIBAL LECTER wrote:

  I am trying to simulate a peptide inside a nanotube and using isotropic

pressure coupling for the system. The nanotube is immersed in a cuboidal
box of water and aligned along the z direction of the box.

The XX, YY components of the stress tensor are about ~570 bars and the
ZZ
component is about -1179 yielding a total pressure of about 2 bars
whereas
my set pressure is ~1.01325 bars. Is this okay or should I be using
semiisotropic coupling?


  Over how long a time period are these values?  If everything is

immersed
in a bath of water, I doubt semiisotropic coupling is necessary.

-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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--
==**

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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--
==

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] Quick question about pressure coupling

2013-09-11 Thread HANNIBAL LECTER 
Yes


On Wed, Sep 11, 2013 at 9:18 AM, Justin Lemkul  wrote:

>
>
> On 9/11/13 9:09 AM, HANNIBAL LECTER wrote:
>
>> 500ps simulations. Yes everything is immersed in a bath of water. Can you
>> please elaborate a little more as to why do you doubt semiisotropic
>> coupling may not be necessary?
>>
>>
> Water should compress isotropically.  I understand where you're coming
> from, given that you have observed a seemingly semiisotropic compression of
> the system, but physically that is not right.  Something like a membrane,
> that has properties that make it sensible to couple x-y and z compression
> separately, would use semiisotropic coupling.
>
> Is this a system in which you're using freezegrps?
>
> -Justin
>
>
>> On Wed, Sep 11, 2013 at 9:05 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 9/11/13 9:01 AM, HANNIBAL LECTER wrote:
>>>
>>>  I am trying to simulate a peptide inside a nanotube and using isotropic
 pressure coupling for the system. The nanotube is immersed in a cuboidal
 box of water and aligned along the z direction of the box.

 The XX, YY components of the stress tensor are about ~570 bars and the
 ZZ
 component is about -1179 yielding a total pressure of about 2 bars
 whereas
 my set pressure is ~1.01325 bars. Is this okay or should I be using
 semiisotropic coupling?


  Over how long a time period are these values?  If everything is
>>> immersed
>>> in a bath of water, I doubt semiisotropic coupling is necessary.
>>>
>>> -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 >> umaryland.edu > | (410)
>>> 706-7441
>>>
>>> ==
>>>
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> >
>>> * Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Search>> Mailing_Lists/Search>before
>>> 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 
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Re: [gmx-users] Quick question about pressure coupling

2013-09-11 Thread Justin Lemkul 



On 9/11/13 9:09 AM, HANNIBAL LECTER wrote:

500ps simulations. Yes everything is immersed in a bath of water. Can you
please elaborate a little more as to why do you doubt semiisotropic
coupling may not be necessary?



Water should compress isotropically.  I understand where you're coming from, 
given that you have observed a seemingly semiisotropic compression of the 
system, but physically that is not right.  Something like a membrane, that has 
properties that make it sensible to couple x-y and z compression separately, 
would use semiisotropic coupling.


Is this a system in which you're using freezegrps?

-Justin



On Wed, Sep 11, 2013 at 9:05 AM, Justin Lemkul  wrote:




On 9/11/13 9:01 AM, HANNIBAL LECTER wrote:


I am trying to simulate a peptide inside a nanotube and using isotropic
pressure coupling for the system. The nanotube is immersed in a cuboidal
box of water and aligned along the z direction of the box.

The XX, YY components of the stress tensor are about ~570 bars and the ZZ
component is about -1179 yielding a total pressure of about 2 bars whereas
my set pressure is ~1.01325 bars. Is this okay or should I be using
semiisotropic coupling?



Over how long a time period are these values?  If everything is immersed
in a bath of water, I doubt semiisotropic coupling is necessary.

-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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--
==

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] Quick question about pressure coupling

2013-09-11 Thread HANNIBAL LECTER 
500ps simulations. Yes everything is immersed in a bath of water. Can you
please elaborate a little more as to why do you doubt semiisotropic
coupling may not be necessary?


On Wed, Sep 11, 2013 at 9:05 AM, Justin Lemkul  wrote:

>
>
> On 9/11/13 9:01 AM, HANNIBAL LECTER wrote:
>
>> I am trying to simulate a peptide inside a nanotube and using isotropic
>> pressure coupling for the system. The nanotube is immersed in a cuboidal
>> box of water and aligned along the z direction of the box.
>>
>> The XX, YY components of the stress tensor are about ~570 bars and the ZZ
>> component is about -1179 yielding a total pressure of about 2 bars whereas
>> my set pressure is ~1.01325 bars. Is this okay or should I be using
>> semiisotropic coupling?
>>
>>
> Over how long a time period are these values?  If everything is immersed
> in a bath of water, I doubt semiisotropic coupling is necessary.
>
> -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!
> * 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] Quick question about pressure coupling

2013-09-11 Thread Justin Lemkul 



On 9/11/13 9:01 AM, HANNIBAL LECTER wrote:

I am trying to simulate a peptide inside a nanotube and using isotropic
pressure coupling for the system. The nanotube is immersed in a cuboidal
box of water and aligned along the z direction of the box.

The XX, YY components of the stress tensor are about ~570 bars and the ZZ
component is about -1179 yielding a total pressure of about 2 bars whereas
my set pressure is ~1.01325 bars. Is this okay or should I be using
semiisotropic coupling?



Over how long a time period are these values?  If everything is immersed in a 
bath of water, I doubt semiisotropic coupling is necessary.


-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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