oguz gurbulak wrote:
Dear Users,
I'm trying to obtain .gro and top files successfuly for my n-alkanes
molecules and want to run md simulations both using oplsaa and Gromos96
force fields seperately. Then I will compare the results of two md runs.
I think that I can generate itp files for Gromos96 force fields using
prodgr server and use them for md. But I sholud write itp files for
each molecules I want to use for oplsaa . Lets say that I produced itp
files, How can I use for example two different itp files and generate a
top file like in below. I'm confused about this. Could you give me the
information about this procedure ?
I don't understand your question. If you create the two .itp files, you do
exactly as is shown below - that's your topol.top. Then include any other
necessary molecule types you may need (water, ions, etc.)
Perhaps you should try running through some simple tutorials (typically
involving proteins) to understand the topology #include mechanism and overall
construction. There are several linked from the wiki.
-Justin
Sincerely
#include "ffoplsaa.itp"
#include "molecule_A.itp"
#include "molecule_B.itp"
[ system ]
packmol system
[ molecules ]
Molecule_A N
Molecule_B N
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
