From: Raisa Carmen Andeme Ela (randemee_at_mtu.edu)
Date: Tue Mar 09 2021 - 15:43:10 CST

Thank you so much, Josh!

I appreciate it! I will confirm I’ve got the correct box.

Sent from my iPhone

> On Mar 9, 2021, at 16:36, Vermaas, Josh <vermaasj_at_msu.edu> wrote:
>
>  Hi Raisa,
>
> Double checking against the ethanol box you are using, (https://urldefense.com/v3/__https://github.com/jvermaas/solventboxgeneration__;!!DZ3fjg!oAKSbWZ_mtJruY3wbNQzry_I26Gux8Dhra9Jtm_LCNeeQGUW9R6upe-7xZAlzULf1w$ , right?), the heavy atoms in ethanol are named C1, C2, O1, and the hydrogens that go along with those heavy atoms. The key selection should be "name C1" or something similar to pick out one of the other heavy atoms.
>
> -Josh
>
>> On 3/9/21 4:31 PM, Raisa Carmen Andeme Ela wrote:
>> Hello VMD community,
>>
>> I’m truly happy to be here!
>>
>> I am new in the Molecular simulation realm, and I’ve been experiencing a couple of issues, I hope you can help me.
>>
>> 1. I’ve used pre-equilibrated ethanol solvent boxes to solvate my molecule in VMD, however, after conducting the solvation using various key selection words such as “name OH, name CB, name C, name OH”, It says successful but I can only visualize the carbon atoms, but not the entire EtOH molecule (please see the image).
>>
>> 2. I’ve tried also using Packmol water/ethanol box (pdb file); when I try to generate the psf file I loose all the ethanol molecules and only the water molecules are visualized.
>>
>> I hope you can give me some tips
>>
>> Thank you so much!
>> <image0.png>
>>
>>
>> Sent from my iPhone
>
> --
> Josh Vermaas
> Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemisty and Molecular Biology
> vermaasj_at_msu.edu
> https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!oAKSbWZ_mtJruY3wbNQzry_I26Gux8Dhra9Jtm_LCNeeQGUW9R6upe-7xZAhR9txew$