• ## Outreach

From: Ropon-Palacios G. (groponp_at_gmail.com)
Date: Mon Aug 09 2021 - 10:58:46 CDT

Thanks so muchs Josh.

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Ropón-Palacios G. BSc., MSc.
Computational biophysicist,
Associate Research,
Laboratorio de Modelagem Computacional,
Departamento de Ciências Exatas,
Universidad Federal de Alfenas, Minas Gerais, Brasil.
Phone: +51 935 055240.
E-mail: groponp_at_gmail.com.

﻿On 8/9/21, 8:00 AM, "Vermaas, Josh" <vermaasj_at_msu.edu> wrote:
In my experience, getting the initial windows exactly right isn't a big
deal. Normally, I make the simplifying assumption that my SMD tracks the
reaction coordinate fairly well (which I can check! Always check this!),
and then I can do something like the following:

mol new system.psf
set minz -20 ; #Depends on your actual range!
set maxz 20 ; #Depends on your actual range!
set numreplicas [expr {\$maxz - \$minz + 1}]; #This assumes 1 Angstrom
spacing.
set asel [atomselect top "all"]
for { set i 0 } { \$i < \$numreplicas } { incr i } {
set frame [expr { int(\$i * [molinfo top get numframes] / \$numreplicas)}]
\$asel frame \$frame
\$asel writenamdbin replica-\$i.coor
pbc writexst replica-\$i.xsc -first \$frame -last \$frame
}

On 8/9/21 12:31 AM, Ropon-Palacios G. wrote:
> Dear users,
>
> made an SMD to generate different windows on the Z + axis, how can I write the files to be able to carry out the simulations of independent windows every 1 Angstrom?
>
>
>
> My biggest problem is how to select for example every 1 angstrom, I have calculated the displacement in Z as (Zi-Z0) throughout the pulling, but I don't know how to make a for that writes every 1 angstrom (xsc and coord ) files

--
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemisty and Molecular Biology
vermaasj_at_msu.edu