[gmx-users] TFE-water simulation

[Archana Sonawani-Jagtap]

Should I start with helical peptides and see if it maintains the helicity
or I can start with random coil?

Do random coil peptides take long simulation time to form helical peptides?

any help on this will be appreciated.


On Tue, Nov 5, 2013 at 12:25 AM, Archana Sonawani-Jagtap <
ask.archana at gmail.com> wrote:

> Thanks Joao Henriques for helping me with the steps.
> On Nov 4, 2013 3:18 PM, "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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>


-- 
Archana Sonawani-Jagtap
Senior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339