[gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

[Justin Lemkul]

On 4/23/15 12:30 AM, mahender singh wrote:
> Thank you dear Justin and Christopher Neale for your help.
>
>   Solute is at -z relative to the bilayer and wants to pull toward +z from the bulk water on the -Z to the +z bulk water through the membrane.
> I observed that the + and the - sign in the pull_coord1_rate is associated with increase or decrease in the COM distance between the pull group and the reference group, respectively.
> I am trying to split simulation into two parts i.e. each leaflet as separate SMD simulation.
> When solute is moving from the -z to the center of the bilayer, it will stop here as pull_coord1_rate = -0.0020 (decrease in the COM, pull force will be - in sign, am I right that sign in force values is negative because decrease in the distance between COM of two group with time is happening), still in the last frame, COM of the molecule will not moves to the +z side and I am not able to do the second part of the simulation by setting pull_start=yes , as if I will change the pull_coord1_rate = 0.0020 it will pull it back in the -z direction (pull force will be in positive sign) (pull_geometry= distance).
>
> @Christopher Neale
> I will try the following setting and will let you know the results.
>
> @ Justin
> When I am pulling the molecule from the center of bilayer to the bulk water and the same molecule from the bulk water to the center of bilayer (by changing the sign in the pull_coord1_rate = -/+0.0020 ). pull-force v/s time graphs are looking like following (first graph is the pulling of molecule from water to the center of bilayer and second graph is from the center of bilayer to the bulk water). My query was the - and the + sign of the pull force, which I think is due to the increase and decrease in the COM distance between the pull group and the reference group, am I right?
>

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-Justin

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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

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