On 7/8/12 6:57 AM, James Starlight wrote:
Justin,
unfortunately my last system have also been crashed after 35ns of
simulation with the links warnings accompanied by the error
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system
Justin,
unfortunately my last system have also been crashed after 35ns of
simulation with the links warnings accompanied by the error
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
For more information
On 7/7/12 11:08 AM, James Starlight wrote:
justin,
It seems that problem was in the big charge groups in the ligand.itp
file. In particularly I've devided largest group into several smaller
and there haven't any crashes been occured yet.
With my last system with the the default COM group I've
justin,
It seems that problem was in the big charge groups in the ligand.itp
file. In particularly I've devided largest group into several smaller
and there haven't any crashes been occured yet.
With my last system with the the default COM group I've obtained crash
on the 25ns with the error abou
On 7/6/12 3:56 PM, James Starlight wrote:
Justin,
I've experimented with 2 dirrerent COM groups
comm-grps = SOL_NA_CL XW Protein_CCl4_ADN ; 3 groups
comm-grps = SOL_NA_CL_XW Protein_CCl4_ADN; 2 groups
but the crashes were in both cases after 12- 15ns of simulation
this time I'v
Justin,
I've experimented with 2 dirrerent COM groups
comm-grps = SOL_NA_CL XW Protein_CCl4_ADN ; 3 groups
comm-grps = SOL_NA_CL_XW Protein_CCl4_ADN; 2 groups
but the crashes were in both cases after 12- 15ns of simulation
this time I've changed to the
comm-grps = System
an
On 7/6/12 2:05 PM, James Starlight wrote:
Justin,
I've done all steps in accordance to your tutorial. I've already done
the same systems with another ligands but had no problem.
This time I've made topology of the ligand via ATB server. I've only
noticed that some cgnr are too big in that to
Justin,
I've done all steps in accordance to your tutorial. I've already done
the same systems with another ligands but had no problem.
This time I've made topology of the ligand via ATB server. I've only
noticed that some cgnr are too big in that topology . This is the
example
ADN 3
[ atom
On 7/6/12 1:12 AM, James Starlight wrote:
Dear Gromacs users!
I have some problems with the simulation of protein-ligand complex
embedded in the ccl4-water environment. In addition there are some
crystallography waters (xw) embedded in the protein interiour of the
protein. I've done equilibrat
Dear Gromacs users!
I have some problems with the simulation of protein-ligand complex
embedded in the ccl4-water environment. In addition there are some
crystallography waters (xw) embedded in the protein interiour of the
protein. I've done equilibration and minimisation of my system and run
it i
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