[gmx-users] regarding editconf

[Ali Khodayari]

Thank you for your response Justin!
I don't really see how it can cause an error, while it might be just a
visualization defect in VMD. 
Previously, I tried to perform each step separately, like doing a centering
by -center 0 0 0, but even performing this step leads to the error "step 0:
Water molecule starting at atom 40225 can not be settled." The only
difference would be a change in the coordinates, no? It is not due to the
fact that I am using 5.1.2 version, is it?
Best regards,
Ali


-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Justin
Lemkul
Sent: dinsdag 15 januari 2019 15:01
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] regarding editconf



On 1/15/19 7:46 AM, Ali Khodayari wrote:
> Dear users,
>
>   
>
> I am trying to reorient and re-center my solute using editconf. 
> Performing such I can place the structure at the desired place, yet it 
> is outside the box when I visualize it in VMD. It leads to an error 
> after mdrun complaining about a water molecule not being settled.
>
> Here is the command I use:
>
> $ gmx editconf -f cell.gro -o cell_newbox.gro -princ -bt triclinic -c 
> -center 0 0 0 -rotate 0 350 0 -n ndx.ndx
>
> Do you see where the problem is?

First, there is no such thing as "outside" an infinite box, so that should
not be the cause of any actual problem.

Regarding editconf, you're doing too many things at once, which may be
mutually exclusive, so you may not be getting what you want. You're telling
editconf to align the longest axis along x (with -princ) but also to rotate
about y (-rotate 0 350 0). Don't do both of those at once.

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================

--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-request at gromacs.org.