[gmx-users] peculiar water behavior

Chetan Mahajan chetanvm10 at gmail.com
Tue Jun 17 23:20:47 CEST 2014 

Thanks, Justin. That makes it clear. I have one small question: I do not
know how does position restraint algorithm work with other things in
gromacs, but  doesn't it generate a lot of stress due to slab moving from
center to near box boundary despite of position restraints, when -com
option is used for refcoord-scaling? If there is a lot of stress, would
this stress affect simulation results?

Thanks and Regards,
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
>>>>>>>
>>>>>>> ==================================================
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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 601
> 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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