Re: [gmx-users] Non-periodic COM Pulling

[Justin Lemkul]

On 7/13/17 1:56 PM, Daniel Kozuch wrote:

Justin,

It was my understanding that direction-periodic would not allow for the NPT
ensemble (which I would like to use if possible, and why I did not use it
in the first place). Is there a way around this?



Not that I'm aware of.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Non-periodic COM Pulling

[Daniel Kozuch]

Justin,

It was my understanding that direction-periodic would not allow for the NPT
ensemble (which I would like to use if possible, and why I did not use it
in the first place). Is there a way around this?

Thanks,
Dan

On Thu, Jul 13, 2017 at 8:58 AM, Justin Lemkul  wrote:

>
>
> On 7/12/17 3:05 PM, Daniel Kozuch wrote:
> > Hello,
> >
> > Is it possible to do non-periodic COM pulling using the distance function
> > in GMX 5.14 (i.e. where the distance between the two groups is calculated
> > ignoring pbc)?
> >
>
> No, but this is what direction-periodic is for.
>
> -Justin
>
> > In the tutorials/online the solution seems to be to simply use a box
> twice
> > the size of the largest pulling distance, but that would be very
> > computationally expensive for me.
> >
> > Best,
> > Dan
> >
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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Re: [gmx-users] Non-periodic COM Pulling

[Justin Lemkul]

On 7/12/17 3:05 PM, Daniel Kozuch wrote:

Hello,

Is it possible to do non-periodic COM pulling using the distance function
in GMX 5.14 (i.e. where the distance between the two groups is calculated
ignoring pbc)?



No, but this is what direction-periodic is for.

-Justin


In the tutorials/online the solution seems to be to simply use a box twice
the size of the largest pulling distance, but that would be very
computationally expensive for me.

Best,
Dan



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Non-periodic COM Pulling

[Daniel Kozuch]

Hello,

Is it possible to do non-periodic COM pulling using the distance function
in GMX 5.14 (i.e. where the distance between the two groups is calculated
ignoring pbc)?

In the tutorials/online the solution seems to be to simply use a box twice
the size of the largest pulling distance, but that would be very
computationally expensive for me.

Best,
Dan
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