16 nov 2012 kl. 22.42 skrev Justin Lemkul:
On 11/16/12 10:45 AM, Gmx QA wrote:
Hello gmx-users,
I've performed a pulling simulation and obtained a force-vs-time plot and a
distance-vs-time plot (xvg-files).
Is it common to somehow combine these to get a force-vs-distance-plot using
a
Hello,
Sorry for bothering you with the same question but just want to make sure that
I am getting my results correctly.
I run simulations where two blocks of ice are in a sliding contact for 5 ns
(using pull code). As an output of the simulation I have pullf.xvg file which I
use for
Hi Erik and Justin
Thanks, writing such a script is easy.
The point of it all would be to be able to map the magnitude of the pulling
force to what I see happen in the pulling simulation. How else would you
get an understanding of what the pulling force means?
Thanks
/PK
The only solution
Hi all.
After using amber03 force field for protein-ligand simulation (pdb2gmx), I
encountered with following error:
Fatal error:
In the chosen force field there is no residue type for 'GLN' as a starting
terminus.
Ligand in my system is a single residue (GLN). There are [GLN], [NGLN] and
On 2012-11-17 15:37, Atila Petrosian wrote:
Hi all.
After using amber03 force field for protein-ligand simulation (pdb2gmx), I
encountered with following error:
Fatal error:
In the chosen force field there is no residue type for 'GLN' as a starting
terminus.
Ligand in my system is a single
On 11/17/12 10:19 AM, shahab shariati wrote:
Dear gromacs users
Can I use two different force fields for a system with 2 components (dna
and carbon nano tube)?
No. Mixing and matching force fields (even if syntactically possible in the
topology) invalidates the force field models.
On 11/17/12 10:37 AM, shahab shariati wrote:
Dear Justin
Thanks for your attention.
You are right but is there a force field which be appropriate for both of
protein and carbon nano tube or dna and carbon nano tube?
What does your search of the literature tell you?
-Justin
--
On 2012-11-17 16:26, Atila Petrosian wrote:
Dear David
Thanks for your quick reply.
You said Add an alanine after the gln then in the top file rename and
remove atoms.
I confused. Why ALA? ALA (alanine) is a residue which is very simple than
GLN structurally.
I should add alanine after the
--
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