Hi Una,
Maybe this answers your question?
http://en.wikipedia.org/wiki/Conjugate_gradient_method
Cheers,
Tsjerk
On Thu, Apr 30, 2009 at 5:00 PM, Una Bjarnadottir
wrote:
> Hi everyone,
>
> In the gromacs manual the equations regarding the conjugate gradient are not
> shown.
>
> Is there anybod
Hi ALL,
I have a protein pdb file. I want to put this protein
molecule in a lipid bilayer using GROMACS. I shall be glad if anyone can kindly
tell me how to build a lipid bilayer in GROMACS and how to embed the protein in
it to get the final pdb of the entire system. Thanks a lot.
Regards,
Anirban Ghosh wrote:
Hi ALL,
I have a protein pdb file. I want to put this protein molecule in a
lipid bilayer using GROMACS. I shall be glad if anyone can kindly tell
me how to build a lipid bilayer in GROMACS and how to embed the protein
in it to get the final pdb of the entire system.
I don't know if this helps you, but there is a membrane plugin for VMD
which you can download for free. I've used this to insert proteins in
membranes and then use namd to run MD. I don't know what steps are
involved to make this structure compatible with GROMACS.
http://www.ks.uiuc.edu/Research/v
Hi,
I am taking a look at reducing the size of my analysis. I've decreased
log writing intervals. I notice mdruns generate these pdb files. Is
there any way of reducing the frequency these files are written? I
think that will go a long way to making my analysis easier.
05/02/2009 07:34 PM
These step*.pdb are written when there is an instability in the system (i.e., on
the verge of a crash). You can usually map them to instances in the .log file
of LINCS warnings or "water molecule could not be settled" reports.
-Justin
Jack Shultz wrote:
Hi,
I am taking a look at reducing
6 matches
Mail list logo
