My understanding is the following:
If you performed a simulation and then analyse it with different values
for 'nrexcl' the results will differ since a different amount of
interactions are excluded. It seems that the exclusion only helps for
'-rdf atom' and not for '-rdf mol_com'.
But the under
Excuseme dear Dr. Tomas, forgiveme the boldness,
I'm new with this, and I dont know who to address
when I have a problem. My name is Hector, and I'm
tryng to install the gromacs software in my computer;
I follewed all the steps in the online manual, however
when I compile Gromacs with the instruc
On 2/19/13 5:04 PM, Thomas Schlesier wrote:
On 2/19/13 3:10 PM, Thomas Schlesier wrote:
> Dear all,
> I have a question regarding g_rdf.
> My system consits of 10 disacchardids (in the following A-B, with
> A-ring/monosaccharid and B-ring/monosaccharid) and i want to determine the
RDF
> (
On 2/19/13 3:10 PM, Thomas Schlesier wrote:
> Dear all,
> I have a question regarding g_rdf.
> My system consits of 10 disacchardids (in the following A-B, with
> A-ring/monosaccharid and B-ring/monosaccharid) and i want to
determine the RDF
> (with flag '-rdf mol_com')for A-A, B-B and the inter
On 2/19/13 3:10 PM, Thomas Schlesier wrote:
Dear all,
I have a question regarding g_rdf.
My system consits of 10 disacchardids (in the following A-B, with
A-ring/monosaccharid and B-ring/monosaccharid) and i want to determine the RDF
(with flag '-rdf mol_com')for A-A, B-B and the intermolekular
Dear all,
I have a question regarding g_rdf.
My system consits of 10 disacchardids (in the following A-B, with
A-ring/monosaccharid and B-ring/monosaccharid) and i want to determine
the RDF (with flag '-rdf mol_com')for A-A, B-B and the intermolekular
for A-B
A-A and B-B is no problem.
But fo
Hi everyone,
I ran a water simulation and I tried to calculate radial distribution
function OO but I get strange peaks from r =1.5nm onwards.
I have 8 atoms in a box of 9.5.
I post the graph as an attached file.
Please does anyone have an idea of what might be going on?
Thanks,
Carla
rdf_
Hi,
I want to get the radial distribution of my system which is composed of a box
of capped alanine residues (CAR). In this respect, I used g_rdf command with
-com option. I chose one of the CAR s as the first, and the others as the
second group. In manual, for -com option, it is written that t
> What is the problem?
Couple of things I would look at first, open the file generated by g_rdf
using a text editor and look at the actual values in there. Then ensure
that what ever you are plotting the data with, is using the correct data
/ columns presented in the data file.
If you still see
OZGE ENGIN wrote:
Hi,
First of all, I wish, everything is o.k for everybody :)
I have a question about the g_rdf command. I read the mailing list but I could not find any problem simiIar to mine. I want to calculate the radial distribution function of my system which consists of tripeptid
Hi,
First of all, I wish, everything is o.k for everybody :)
I have a question about the g_rdf command. I read the mailing list but I could
not find any problem simiIar to mine. I want to calculate the radial
distribution function of my system which consists of tripeptide and water
molecule
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