On 10/8/12 12:48 AM, shika wrote:
it is because when i put
genbox -cp protein_box.gro -ci solvent.gro -nmol 1381 -p control.top
-o prot_solv.gro
the error turn out like this :
System total charge: 0.000
Grid: 17 x 16 x 14 cells
nri = 12718, nrj = 100152
Try 9119box_margin = 0.45overlap:
Killed
thats why i need to run genbox twice
Sorry, read the original message too quickly and thought the solvent
configuration was the same both times. My mistake :)
The error you receive is a result of genbox failing to do what you're asking.
You've exhausted the memory available, suggesting that there is no way to add
that many molecules of whatever solvent into the box. Either set a larger box
with editconf prior to this step, or try to insert fewer molecules.
-Justin
On Mon, Oct 8, 2012 at 9:21 AM, Justin Lemkul [via GROMACS]
<[email protected]> wrote:
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]
<[hidden email]> 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
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========================================
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Virginia Tech
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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