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

[Mohamed Abdelaal]

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 ?

Thanks,
Mohamed