On 3/27/13 11:32 PM, sdshine wrote:
Dear all,
Does that mean the atoms will shrink and adjust at the time inflategro step
and
this closely packed lipids will stay apart? Because as you said the energy
of course will be high on selected atoms during first EM step.
Could you suggest me that, can I proceed as such with my system, since there
is no problem in grompp and EM step (except high energy on some atom).
or Do I need to manually remove those overlapping lipids and water
molecules.
No, InflateGRO does this for you. After inflation, there should be no water in
the system and the lipids should have expanded outward. Any that were too close
(as defined by the cutoff specified on the command line) should have been deleted.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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://lists.gromacs.org/mailman/listinfo/gmx-users
* 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 gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
