On 7/31/13 12:18 PM, George Patargias wrote:
Hi Justin
Yes, it does look like Fig. 8.3 in the manual if I choose the OW atoms as
the the two groups!
So there must be a problem with the choice water-water or SOL-SOL for RDF
groups.
Indeed there would, because then (with -rdf atom) you're calculating an RDF for
all possible atom pairs when choosing whole molecules.
-Justin
> Many thanks!
>
On 7/31/13 10:49 AM, George Patargias wrote:
Hello
I am trying to calculate the RDF of water with water for a 10 ns MD of
pure SPC water simulation (3x3x3 nm box). I run g_rdf with the default
-rdf option (atom).
The problem is that the integration of the RDF curve up to the first
minimum yields a zero value which is obviously not right
Do you have any suggestions about this? Should I run g_rdf in a
different
way?
Impossible to tell without seeing the RDF itself. If it doesn't look like
Figure 8.3 in the manual, then you've got a problem either with the
simulation
itself or the way the RDF was calculated. If it does, then you've got a
problem
with how you're integrating the curve.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
--
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
Dr. George Patargias
Postdoctoral Researcher
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece
Office: +302106597568
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
--
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
