leila separdar wrote:
I have .gro and .top of a nanoparticle at temperature 1K and I want to
add the simulation box some other atomes at temperature 300K. is there
any body knows how can I do it. I have used (genbox -cp
nanoparticle.gro -ci otheratom.gro -p nanoparticle.top -o out) but it
add more than atomes than I expect for example if there is 600 other
atomes in otheratom,gro file this command add 2000 atomes to
simulation box and also nanoparticle.top does not update.
thanks in advance
The -ci option should be used in conjunction with -nmol, and the configuration
contained in -ci (I believe) cannot contain multiple molecules. If you want 600
molecules/atom to be inserted, provide a configuration of a single molecule/atom
and specify -nmol 600.
With respect to the topology not being updated, that is to be expected. The -p
option only works for water (unfortunately).
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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