[gmx-users] Re: Fwd: How to can i replace a molecule
jalemkul at vt.edu
Mon Oct 8 03:19:30 CEST 2012
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.
> On Mon, Oct 8, 2012 at 8:59 AM, Justin Lemkul [via GROMACS]
> <ml-node+s5086n5001764h68 at n6.nabble.com> 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
>>> 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:
>> A more robust approach for dealing with mixed systems can be found here:
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> gmx-users mailing list [hidden email]
>> * 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
>> To start a new topic under GROMACS Users Forum, email
>> ml-node+s5086n4370410h94 at n6.nabble.com
>> To unsubscribe from GROMACS, click here.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users