[gmx-users] All bulk is moving during Umbrella sampling

[gozde ergin]

Justin, thank you for the advice.

But if I apply a force to keep molecules within a layer, how I will extract
this force effect on PMF?

On Sun, Jun 7, 2015 at 3:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/6/15 2:57 PM, gozde ergin wrote:
>
>> Actually I know I need to do something like this however I don't know how
>> to do it.
>> Could anybody give a hint how this approach can be realized in GROMACS?
>> I could not find a clear answer in manual.
>>
>>
> The key is the definition of the restraint reference coordinates.  To keep
> molecules within a layer from zero to some value z, you need to create a
> reference coordinate file in which the z-coordinate of the restrained atoms
> are all equal to z/2, such that the restraint will take effect at +z and
> zero.  This coordinate file is only to be used for grompp -r as it is
> obviously nonphysical, but it defines the reference positions for the
> restraints.
>
> Then set the correct "layer" geometry (g=5 for a layer along z) and
> specify the value of z at which the restraint is applied.  This also needs
> to be done with no pressure coupling along z, which is probably the case
> already for what you're doing.
>
> -Justin
>
>
>  On Thu, Jun 4, 2015 at 6:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 6/4/15 10:43 AM, gozde ergin wrote:
>>>
>>>  Hi all,
>>>>
>>>> I am doing some umbrella sampling simulation in order to estimate the
>>>> PMF
>>>> profile of the system.
>>>> While doing this simulations I did:
>>>>
>>>> -- Simulated the system in x*y*z box.
>>>> -- In order to have a gas phase I expanded the z coordinate to 5z and
>>>> simulate the system in x*y*5z
>>>> -- Minimization
>>>> -- Equilibration
>>>> -- Pulling
>>>> -- Than umbrella sampling.
>>>>
>>>> During the umbrella sampling all of bulk molecules moved on z direction.
>>>> However the distances between the COM of pulled molecule and COM of mass
>>>> stays constant. It is not a big problem for estimating the PMF but it
>>>> is a
>>>> problem when I want to calculate the pressure and density profile of the
>>>> system.
>>>>
>>>> Do you have any suggestion to prevent the bulk molecules moving inside
>>>> the
>>>> box?
>>>>
>>>>
>>>>  Use a flat-bottom restraint to confine the bulk to one region of the
>>> box.
>>> Otherwise, they will naturally have a tendency to fill up the available
>>> space.
>>>
>>> -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
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
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> --
> ==================================================
>
> 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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> Gromacs Users mailing list
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