toby10222...@sina.com wrote:
Dear all:
I am trying to insert a certain number of water molecules into a
nanotube with Gromacs-4.0.5.
When I input the command "genbox -cp tube.gro -ci spc216.gro -nmol 328
-try 20 -o",
I get the following error.
Program genbox, VERSION 4.0.5
Source code file: gmx_genbox.c, line: 318
Fatal error:
more then one residue in insert molecules
program terminated
Should the insert molecules be no more than one residue?
You are using a file (spc216.gro) that contains 216 residues, not one, so
Gromacs is crashing.
If it should be, how can I insert 328 water molecules into the tube?
Are there any other commands in Gromacs that can be used for the same thing?
Two options:
genbox -cp -cs spc216.gro -maxsol 328
or obtain a water.gro that contains 1 water molecule and
genbox -cp -ci water.gro -nmol 328
-Justin
Thank you in advance!
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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