On 10/7/12 9:17 PM, shika wrote:
Thanks Justin.
May I ask something, if i'm using the command for genbox before
minimization which is
genbox -cp protein_box.gro -cs solvent.gro -p control.top -o prot_solv.gro
next i insert water by using same command;
genbox -cp prot_solv.gro -p control.top -cs spc216.gro -o
prot_solv_wtr.gro maxsol 350
i'm using -cs for both genbox command instead of -ci -nmol, is it
wrong to use the command like that?
I don't understand why you need two invocations of genbox, but syntactically the
commands are correct. The -ci -nmol options are for adding molecules randomly
in the unit cell. The -cs option is for stacking grids of water boxes (or
whatever other solvent you provide) within the unit cell.
-Justin
On Mon, Oct 8, 2012 at 8:59 AM, Justin Lemkul [via GROMACS]
<[email protected]> wrote:
On 10/7/12 3:52 PM, Ali Alizadeh wrote:
Dear All users
How to can i replace a molecule(for example methane) with another
molecule(propane)?
Number of these molecules are given and their position is random,
Can I use genbox or genion, How to do i do it?
Likely you can't, as you were already advised:
http://lists.gromacs.org/pipermail/gmx-users/2012-October/075338.html
A more robust approach for dealing with mixed systems can be found here:
http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [hidden email]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [hidden email].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
________________________________
If you reply to this email, your message will be added to the discussion
below:
http://gromacs.5086.n6.nabble.com/How-to-can-i-replace-a-molecule-tp5001756p5001764.html
To start a new topic under GROMACS Users Forum, email
[email protected]
To unsubscribe from GROMACS, click here.
NAML
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
