[gmx-users] GMO simulation

[Justin Lemkul]

Please don't reply to the whole digest.

On 4/14/19 6:08 AM, Ayesha Fatima wrote:
> Thank you Rahul for the response. I tried that but still cant see it.
>
> In addition to my previous question,. how do we restrain the lipid membrane
> in one direction only. I came across the GROMACS documentation where it
> sytes the freedim parameter. Is it placed in the pull md parameter file of
> elsewhere?
> Thank you
>

You do not want freezedim; freezing is a severe perturbation and is 
unphysical (though it does have its uses in certain situations).

The position-restrain a bilayer to a plane, apply a restraining force 
only in one dimension, e.g. z if the membrane plane is in x-y:

[position_restraints]
; atom  type  fx   fy  fz
   N     1     0    0   1000

where N is the atom number to be restrained (e.g. P in a phospholipid)

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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