[gmx-users] gmx_mpi insert-molecules

[Justin Lemkul]

On 10/25/16 8:01 AM, shahab shariati wrote:
> Dear gromacs users,
>
> I want to do md similation of 10 small molecules in water. To this aim, I
> used following commands:
>
> gmx_mpi editconf -f a.pdb -center 0 0 0 -o b.pdb
>

There is no reason to do this; GROMACS centers all boxes at the middle of the 
vectors and mdrun will immediately re-wrap the coordinates.

> gmx_mpi insert-molecules -ci b.pdb -o c.gro -nmol 10 -box 10 10 10
>
> I have 3 questions:
>
> 1) Is my manner true?
>

As stated above, your editconf command really isn't doing anything useful for you.

> 2) For 10 molecules, which dimention of box is appropriate?
>

What concentration do you want to model?  For 10 small molecules, if they really 
are "small" (a few dozen atoms maybe? How big are they?) then a 10-nm cube is 
overkill.

> 3) When I see c.gro using vmd, the part of some molecules are put out of
> box.
>

There is no such thing as "outside" a periodic box.  But you centered at 
(0,0,0), which is normally the "corner" of the central unit cell in GROMACS 
convention, so things are probably going to look a little weird when you 
visualize the coordinates.

-Justin

>
> https://td2ec2in5euwest.teamdrive.net/primespace/public/77350/4MQPVS000T2QS0057UNJ7CHP22TZF9G9/c.gro
>
> https://td2ec2in5euwest.teamdrive.net/primespace/public/77350/TZKXARG00T2QS0057UNJK110Y2TZF9GM/c.jpg
>
> Please guide me about that.
>
> Best, Shahab
>

-- 
==================================================

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

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