I will attempt an answer, however there might be a better response. It depends on your input .xvg (what the first column is) and what you are telling it to do (defualt is time), and if these correspond to your time frames (can be timepoint or siply frame # I believe). g_sham seems (to me) to w
How long are you simulating for? Have you looked at the rmsf?
On 15 Dec 2013, at 18:42, xiao wrote:
> Dear all,
>
> I am doing a MD on a mutant protein which is unstable from exprient. However,
> i found no difference between the wild type and the mutant protein from md,
> the structure and t
On Sun, Dec 15, 2013 at 1:42 PM, xiao wrote:
> Dear all,
>
> I am doing a MD on a mutant protein which is unstable from exprient.
> However, i found no difference between the wild type and the mutant protein
> from md, the structure and the rmsd are very similar in the mutant and the
> wild type.
What exactly is the mutation?
Length of the MD run?
Have you tried clustering and compare the clustered structure?
On Sun, Dec 15, 2013 at 10:42 AM, xiao wrote:
> Dear all,
>
> I am doing a MD on a mutant protein which is unstable from exprient.
> However, i found no difference between the wi
Dear all,
I am doing a MD on a mutant protein which is unstable from exprient. However, i
found no difference between the wild type and the mutant protein from md, the
structure and the rmsd are very similar in the mutant and the wild type.
Can anyone tell me how to tackle this problem?
Bes
On Sun, Dec 15, 2013 at 3:20 AM, Andrew Bostick
wrote:
> Dear Gromacs users
>
> I have following error when I do equilibration:
>
> There is no domain decomposition for 4 nodes that is compatible with
> the given box and a minimum cell size of 0.8875 nm Change the number of
> nodes or mdrun option
Hi,
I had a query regarding the bin files generated by g_sham.
Does the bin index contain timepoints? i.e. there are 1024 bins so each bin
has a number of time points? And supposes bin 756 has numbers like 3876,
20020, 7896 so these would all correspond to time and we could then dump
the represent
Dear Gromacs users
I have following error when I do equilibration:
There is no domain decomposition for 4 nodes that is compatible with
the given box and a minimum cell size of 0.8875 nm Change the number of
nodes or mdrun option -rcon or -dds or your LINCS settings.
I tried all suggestios in ab
