On 8/16/12 4:19 PM, tdgrant1 wrote:
No they do not. The trajectory contains all the atoms, including the solvent
(~300,000 atoms), whereas the structure passed to -s is the averaged
structure from the last 60ns of simulation and only includes the non-solvent
atoms (~15,000). Should I rerun rm
No they do not. The trajectory contains all the atoms, including the solvent
(~300,000 atoms), whereas the structure passed to -s is the averaged
structure from the last 60ns of simulation and only includes the non-solvent
atoms (~15,000). Should I rerun rmsf on the last 60ns but select System
in
On 8/16/12 4:11 PM, tdgrant1 wrote:
This "System" as described by group 0 in the previous message is actually
only the solute, a protein-tRNA complex of ~15000 atoms. I tried running
only the backbone and even only c-alphas (808 atoms total) and I still
received a segmentation fault.
Do the
This "System" as described by group 0 in the previous message is actually
only the solute, a protein-tRNA complex of ~15000 atoms. I tried running
only the backbone and even only c-alphas (808 atoms total) and I still
received a segmentation fault.
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On 8/16/12 3:54 PM, tdgrant1 wrote:
Oh okay, thanks. I didn't realize warnings were just that, only warnings and
didn't stop the program. The program did not finish however, and the
problem was a Segmentation Fault. The output literally was:
Select a group: 0
Selected 0: 'System'
Reading fr
Oh okay, thanks. I didn't realize warnings were just that, only warnings and
didn't stop the program. The program did not finish however, and the
problem was a Segmentation Fault. The output literally was:
Select a group: 0
Selected 0: 'System'
Reading frame 0 time0.000
WARNING: if
On 8/16/12 3:19 PM, tdgrant1 wrote:
Hi Justin,
I did indeed correct for periodic boundary conditions prior to running rmsf,
so I'm not sure what the problem would be there.
The message you got was a warning, not an error. The warning is generic and is
printed by any Gromacs program that d
Hi Justin,
I did indeed correct for periodic boundary conditions prior to running rmsf,
so I'm not sure what the problem would be there.
Is there any way of producing an average structure from rmsf (or any other
program for that matter) that is not output as a .pdb file but as a .tpr
file?
T
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