[gmx-users] changing the location of a molecule in a box

[Justin Lemkul]

On 9/9/16 7:59 AM, Smith, Micholas D. wrote:
> HI Anurag Dobhal,
>
> If it is already split into two regions when you simulate without the protein, load the system in something like VMD, define a sphere between the two solvents that can hold your protein, record the residue ids for the water/chloroform in that sphere region, delete these from your .gro file, and place your protein in that position using a text editor. Then use editconf to make sure all of the atom numberings are resolved. Then run a short NPT simulation with the protein fixed in place to let the solvent molecules relax around it (since you may have created voids during the placement/removal of solvent molecules).
>
> There may be more direct ways, but that's how others I've worked with have made void regions to place proteins in specific locations for initial simulation starting configurations.
>

If the pre-equilibrated biphasic system is of correct size to accommodate the 
protein, it's trivial in GROMACS.  Center the protein in a box of that size with 
editconf, and use solvate with the two-solvent system to fill the box.

-Justin

> ===================
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Anurag Dobhal <anurag.dobhal at nano-medicine.co.in>
> Sent: Friday, September 09, 2016 6:55 AM
> To: gromacs.org_gmx-users at maillist.sys.kth.se; gmx-users at gromacs.org
> Subject: Re: [gmx-users] changing the location of a molecule in a box
>
> Dear Gromacs users,
>
> I am working on a biphasic system where I have taken chloroform and water
> as two solvents. I want to locate my protien at the center of the box such
> that half of the protien is solvated in water and other half in the
> chloroform.
>
> How can I acheive the desired placement of the protien.
>
> Thank You
>
>
>
>
> *Anurag Dobhal*
> *Graduate Student (Bioprocess Technology)*
>
>
> On Fri, Sep 9, 2016 at 4:24 PM, Anurag Dobhal <
> anurag.dobhal at nano-medicine.co.in> wrote:
>
>> Dear Gromacs users,
>>
>> I am working on a biphasic system where I have taken chloroform and water
>> as two solvents. I want to locate my protien at the center of the box such
>> that half of the protien is solvated in water and other half in the water.
>>
>> How can I acheive the desired placement of the protien.
>>
>> Thank You
>>
>>
>>
>> *Anurag Dobhal*
>> *Graduate Student (Bioprocess Technology)*
>>
>>
>>
>
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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

==================================================