[gmx-users] peculiar water behavior

Chetan Mahajan chetanvm10 at gmail.com
Tue Jun 17 23:56:07 CEST 2014 

*Forgot to comment:*

*So you are saying:  because it is more forgiving, we are observing slab
movement in a run with "com" option for refcoord scaling, and NOT in "all"
option...as such, choosing any one of options "com" or "all" for refcoord
scaling should not matter simulation results point of view, despite of
difference in slab movement observation?*

Thanks
Chetan

On Tue, Jun 17, 2014 at 10:01 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/17/14, 10:32 AM, Chetan Mahajan wrote:
>
>> Any ideas :
>>
>> 1. why slab is moving despite of position constraints?
>>
>>
> Restraints are biasing potentials; they don't prevent movement.  Why is it
> necessary that your slab not move?
>
>
>  2. That too, only with "com" option of refcoord scaling...with "all"
>> option
>> slab does not move...
>>
>>
> Using "all" means the restraint reference for each atom is the original
> position in the input coordinates, with respect to every atom individually.
>  It is more stringent, though it can often be unstable.  The "com" option
> means the restraint potential is calculated with respect to the COM of the
> group of restrained atoms; it is a bit more forgiving, since the COM might
> only move slightly, even if there are relatively larger changes in the
> individual atomic positions.
>
> -Justin
>
>

>  Thanks
>>
>>
>> On Sun, Jun 15, 2014 at 7:02 PM, Chetan Mahajan <chetanvm10 at gmail.com>
>> wrote:
>>
>>  The pics should be seen in the reverse order. Due to sorting by name,
>>> "After equilibration" pic occurs first.
>>>
>>>
>>> On Sun, Jun 15, 2014 at 6:54 PM, Chetan Mahajan <chetanvm10 at gmail.com>
>>> wrote:
>>>
>>>  Thanks.
>>>>
>>>> No, same things do not happen when it's a NVT simulation or no mixed
>>>> potentials. Also, with mixed potentials in NPT simulation, this things
>>>> of
>>>> slab moving in one direction (thus following water movement) happens
>>>> only
>>>> with -com option of refcoord-scaling, *not with -all option for
>>>> refcoord-scaling. *
>>>>
>>>>
>>>> I have a crystal slab with equal amount of water on both the sides.
>>>> During NPT equilibration (with refcoord-scaling option of -com, not
>>>> -all),
>>>> some water on side side of the slab enters opposite side due to periodic
>>>> boundary conditions I have (say water on the right side of the slab,
>>>> crosses boundary of the box and enter the left side of the slab due to
>>>> periodic boundaries. Even crystal slab follows this water and move same
>>>> distance in the same direction of water movement. Following link shares
>>>> pictures of the solvated slab before and after equilibration:
>>>>
>>>>
>>>> https://www.dropbox.com/sh/tjq80jgnff1y7ur/AAAzhnv8uwl-UMQ0TYx8PuPAa
>>>>
>>>> I feel, this is not an error, but it is odd. Due to periodicity we have,
>>>> output of any calculations will remain the same.  Again, with -all
>>>> option
>>>> for refcoord scaling, this movement of water and slab DOES NOT occur.
>>>>
>>>> Thanks a lot!
>>>> regards
>>>> Chetan
>>>>
>>>>
>>>> On Sat, Jun 14, 2014 at 4:40 AM, Mark Abraham <mark.j.abraham at gmail.com
>>>> >
>>>> wrote:
>>>>
>>>>  Hi,
>>>>>
>>>>> Repeating myself - simplify things! Do sane things happen with NVT?
>>>>> With
>>>>> no
>>>>> mixed potentials?
>>>>>
>>>>> Your words aren't making sense to me - you'll do much better with
>>>>> pictures,
>>>>> making sure you turn on your visualizer's option to show the periodic
>>>>> box.
>>>>>
>>>>> Mark
>>>>>
>>>>>
>>>>> On Fri, Jun 13, 2014 at 8:45 PM, Chetan Mahajan <chetanvm10 at gmail.com>
>>>>> wrote:
>>>>>
>>>>>  Hi Justin,
>>>>>>
>>>>>> I, actually, do not want to preserve any voids. Initial void that I
>>>>>> mentioned is supposed to be filled by water during equilibration and
>>>>>> it
>>>>>> does so. However, problem is that some or major quantity of water
>>>>>>
>>>>> moves out
>>>>>
>>>>>> from one side of the box to enter from the opposite side (obeying
>>>>>>
>>>>> periodic
>>>>>
>>>>>> boundary conditions) and crystal slab moving following water movement.
>>>>>>
>>>>> Thus
>>>>>
>>>>>> although initially there is almost equal amount of water on both sides
>>>>>>
>>>>> of
>>>>>
>>>>>> the slab, we have more water on one side of the slab than the other
>>>>>>
>>>>> side
>>>>>
>>>>>> after equilibration. In other words, length of the box on one side of
>>>>>>
>>>>> the
>>>>>
>>>>>> slab is more than the other side after equilibration, although it is
>>>>>>
>>>>> same
>>>>>
>>>>>> on both sides before equilibration. My dilemma is whether this is due
>>>>>>
>>>>> to
>>>>>
>>>>>> pressure coupling or any gromacs thing or due to potentials (mixed
>>>>>> buckingham and LJ)?
>>>>>>
>>>>>> Thanks
>>>>>> Chetan
>>>>>>
>>>>>>
>>>>>> On Fri, Jun 13, 2014 at 7:43 AM, Justin Lemkul <jalemkul at vt.edu>
>>>>>>
>>>>> wrote:
>>>>>
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> On 6/12/14, 11:15 PM, Chetan Mahajan wrote:
>>>>>>>
>>>>>>>  Dear All,
>>>>>>>>
>>>>>>>> I am simulating TiO2 crystal solvated by water  and ions like
>>>>>>>>
>>>>>>> sodium and
>>>>>
>>>>>> formate. I am observing one peculiar thing, and I would like to
>>>>>>>>
>>>>>>> rectify
>>>>>
>>>>>> that. I have initial structure of crystal slab at the center of the
>>>>>>>>
>>>>>>> box
>>>>>
>>>>>> elongated in z-direction and almost equal boxlength on both the
>>>>>>>>
>>>>>>> sides,
>>>>>
>>>>>> with
>>>>>>>> a gap of 1 nm between slab surface and first layer of water close to
>>>>>>>>
>>>>>>> slab.
>>>>>>
>>>>>>>    This space is kept to avoid water going on the sides of the
>>>>>>>>
>>>>>>> crystal
>>>>>
>>>>>> during
>>>>>>>> equilibration. This was a minor information. Now, the main
>>>>>>>>
>>>>>>> observation
>>>>>
>>>>>> is
>>>>>>
>>>>>>> that during NPT equilibration, water from one side of the slab
>>>>>>>>
>>>>>>> enters
>>>>>
>>>>>> the
>>>>>>
>>>>>>> other opposite side of the slab (using periodic conditions) so that
>>>>>>>> boxlengths on both sides of the slab are very different at the end
>>>>>>>>
>>>>>>> of
>>>>>
>>>>>> equilibration. Is this an artifact of pressure coupling? Following
>>>>>>>>
>>>>>>> is my
>>>>>
>>>>>> equilibration .mdp file. I have tried varying the compressibility
>>>>>>>>
>>>>>>> and
>>>>>
>>>>>> tau-p
>>>>>>>> parameters in the following file. e.g. zero compressibility in x/y
>>>>>>>> direction or tau-p reduced to 3.
>>>>>>>>
>>>>>>>>
>>>>>>> With pressure coupling, any voids present in the system will be
>>>>>>> compressed.  If you need to try to preserve some sort of vacuum
>>>>>>>
>>>>>> layers,
>>>>>
>>>>>> use
>>>>>>
>>>>>>> NVT.
>>>>>>>
>>>>>>> -Justin
>>>>>>>
>>>>>>> --
>>>>>>> ==================================================
>>>>>>>
>>>>>>> Justin A. Lemkul, Ph.D.
>>>>>>> Ruth L. Kirschstein NRSA 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 | (410) 706-7441
>>>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>>>
>>>>>>> ==================================================
>>>>>>> --
>>>>>>> Gromacs Users mailing list
>>>>>>>
>>>>>>> * Please search the archive at http://www.gromacs.org/
>>>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>>>>>
>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>
>>>>>>> * For (un)subscribe requests visit
>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>>>>>
>>>>>> or
>>>>>
>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>
>>>>>>>  --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>> posting!
>>>>>>
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>
>>>>>> * For (un)subscribe requests visit
>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>
>>>>>>  --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>> posting!
>>>>>
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>> * For (un)subscribe requests visit
>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>>>
>>>>
>>>>
>>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA 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 | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

More information about the gromacs.org_gmx-users mailing list