[gmx-users] TFE-water simulation

[João Henriques]

Erratum:

Where I wrote "I ended up going with the former" it should be "I ended up
going with the latter".

/J


On Mon, Nov 4, 2013 at 10:47 AM, João Henriques <
joao.henriques.32353 at gmail.com> wrote:

> Hello Archana,
>
> I'm also toying with a TFE-water system, therefore I am also a newbie.
> This is what I am doing, I hope it helps:
>
> 1) Since I'm using G54A7 I created a TFE.itp using GROMOS parameters (I
> don't use PRODGR, see why in DOI: 10.1021/ci100335w).
> 2) Do the math and check how many molecules of TFE you're going to need
> for a given v/v TFE-water ratio and a given simulation box volume.
> 3) Build box with the correct size.
> 4) Randomly insert correct number of TFE molecules.
> 5) Solvate.
> 6) Insert protein.
>
> Hopefully, the amount of TFE and water molecules that will be deleted in
> inserting the protein in the final step will be proportional, given that
> the TFE molecules are well distributed.
>
> I've tried many different ways of doing this and it's always impossible to
> maintain a perfect TFE-water ratio, no matter the order and manner of
> insertion of each system component. I've also never been able to insert the
> correct number of waters after the TFE. My calculations predict a higher
> number, but the solvation algorithm can't find enough space for them.
>
> In sum, either you place each molecule by hand and you spend a life time
> building the system, or you just make a few compromises and deal with it. I
> ended up going with the former as I have a limited amount of time on my
> hands and I am aware of the approximations I am doing.
>
> Best regards,
>
> João Henriques
> ------------------------------------------------
> PhD student
> Division of Theoretical Chemistry
> Lund University
> Lund, Sweden
> ------------------------------------------------
> joao.henriques at teokem.lu.se
> http://www.teokem.lu.se/~joaoh/
>
>
> On Thu, Oct 24, 2013 at 7:15 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 10/24/13 1:13 PM, Archana Sonawani-Jagtap wrote:
>>
>>> Dear Justin,
>>>
>>> I have not constructed the system but I have downloaded it from ATB
>>> website. To maintain the number of TFE and water molecules(1:1 v/v) in
>>> the
>>> system (I don't want to add extra water molecules) I tried many options
>>> in
>>> genbox but still it adds 678 water molecules. Can you provide me some
>>> hint?
>>>
>>>
>> Not without seeing your actual command(s).
>>
>>
>>  Is their need to remove periodicity of this pre-equilibrated system as in
>>> case of lipids?
>>>
>>>
>> No idea.  Are the molecules broken in the initial configuration?
>>
>> -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 | (410) 706-7441
>>
>> ==================================================
>>
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>
>