pol...@huji.ac.il wrote:
While trying to search throw mailing list I'm getting the next error
"/content/body/p[2]/span, function 'RecordList' failed "
The site is intermittently buggy, although it seems to be working fine now.
I'm not interested in basic information. I'm using "g_rdf -f xxxx.trr -s
topol.tpr -rdf atom" to get rdf of water oxygens around a protein. As a
reference group I'm choosing "protein" and as a group I'm using "SOL".
If you're choosing "SOL" as the the calculation group with "-rdf atom" I don't
know if that will work. Typically, you'd create an index group for "OW" atoms
in water in order to use an atom-based RDF. You may also be interested in the
-com option, if you'd like to generate an RDF based on the COM of the protein,
since the whole molecule is your reference.
The command line for getting rdf of solute COM I use "g_rdf -f xxxx.trr
-s topol.tpr -rdf mol_com". As a reference group I'm choosing "protein"
and as a group I'm using "SRB" when SRB is a solute name. So first of
all I'm trying to understand if I'm doing the right thing. Second, for
Seems to be right, aside from the above comment.
g(r) we need the local density to be divided by the average density in
infinite solution (or bulk). How does the algorithm work? I understand
that for local density it calculates the number of molecules but what
about the bulk or whatever the algorithm uses.
See the manual, section 8.4.
-Justin
Thanks a lot in advance.
Regina
The gromacs version I'm using is 4.0.3
Justin A. Lemkul wrote:
Justin A. Lemkul wrote:
pol...@fh.huji.ac.il wrote:
Dear gromacs users,
I want to calculate radial distribution function around my protein.
I want to get g_rdf for water molecules (OW) around my protein and
g_rdf for COM of some solutes around my protein. The numbers should
be averaged over all the frames. I tried to look at the mailing list
but there is some error and as a result I can't open it. Can someone
help me with it and give me the command I should use.
The manual and the -h flag should give you the basic information you
need to run g_rdf. If there has been "some error" it is useless to
say so. What error did you receive? What was the command line that
you tried that gave rise to the error? What Gromacs version are you
using?
-Justin
Regina
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pol...@fh.huji.ac.il wrote:
Dear gromacs users,
I want to calculate radial distribution function around my protein. I
want to get g_rdf for water molecules (OW) around my protein and
g_rdf for COM of some solutes around my protein. The numbers should
be averaged over all the frames. I tried to look at the mailing list
but there is some error and as a result I can't open it. Can someone
help me with it and give me the command I should use.
The manual and the -h flag should give you the basic information you
need to run g_rdf. If there has been "some error" it is useless to
say so. What error did you receive? What was the command line that
you tried that gave rise to the error? What Gromacs version are you
using?
-Justin
Regina
----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.
--
========================================
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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