[gmx-users] Does the energy minimization deals with velocity ?

[Justin Lemkul]

On 4/17/20 11:06 AM, Mohamed Abdelaal wrote:
> Hello everyone,
>
> If I will add the velocity manually to my system, should I add them before
> the energy minimization or after ?
>
> I will do the below steps:
>
> 1. insert molecules
> 2. energy minimization
> 3. NVT equilibiration
> 4. NPT equilibiration
> 5. production run.
>
> should I add the velocity before the NVT equilibiration step or before the
> energy minimization ?
>
> I am trying to reproduce the results of the below paper:
> Title: Morphology of a Bulk Heterojunction Photovoltaic Cell with Low Donor
> Concentration
> Authors: Thomas Lee, † Audrey Sanzogni, † Ningxin Zhangzhou, † Paul L.
> Burn,* ,†,‡ and Alan E. Mark* ,†
> Paragraph:
> All deposition simulations were performed using the GROMACS simulation
> package version 4.6. 27. During the deposition process, new molecules were
> inserted 2 nm from the top of the film every 10 ps with a random
> orientation and an initial velocity toward the surface to ensure they reach
> the growing film. The net velocity was randomly selected from a normal
> distribution with a mean of 0.05 nm ps −1 and a standard deviation of
> square root ( k B T / m)  where m is the mass of the molecule. Molecules
> that were more than 1 nm above the top of the film and moving away from the
> substrate (after having bounced on impact or sublimed from the surface) *were
> removed prior to the insertion of the next molecule.*
>
> The highlighted paragraph means that each inserted molecule had the time to
> move until it reaches the growing film before inserting the next molecule.
> I thought I can do that by  doing energy minimization between single
> molecules insertion. But if the molecules will not move during the energy
> minimization then how can I allow each molecule to move to the growing
> molecule before inserting the next molecule ?

Energy minimization is not a dynamical process. It is performed at 0 K 
and there are no velocities.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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