[gmx-users] Quick question about pressure coupling

[HANNIBAL LECTER]

Yes


On Wed, Sep 11, 2013 at 9:18 AM, Justin Lemkul <jalemkul at vt.edu> 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 <jalemkul at vt.edu> 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 at outerbanks.umaryland.****edu <jalemkul at outerbanks.**
>>> umaryland.edu <jalemkul at outerbanks.umaryland.edu>> | (410)
>>> 706-7441
>>>
>>> ==============================****====================
>>>
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users>
>>> <htt**p://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<h**ttp://www.gromacs.org/Support/**
>>> Mailing_Lists/Search<http://www.gromacs.org/Support/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-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists>
>>> <http://**www.gromacs.org/Support/**Mailing_Lists<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 at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
>
> ==============================**====================
> --
> gmx-users mailing list    gmx-users at 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<http://www.gromacs.org/Support/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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>