On Thu, Apr 19, 2018 at 8:44 AM, Alexander Alexander
<alexanderwie...@gmail.com> wrote:
> Hi Christoph,
>
> On Thursday, April 19, 2018 at 12:19:49 AM UTC-4, Christoph Junghans wrote:
>>
>> On Wed, Apr 18, 2018 at 9:39 PM, Alexander Alexander
>> <alexand...@gmail.com> wrote:
>> > Hi
>> > Any ideas please?
>> Sorry, there was no question in your previous email, so I thought it
>> was just FYI.
>>
>> Honestly I haven't seen that kind of issue before.
>> Try to set the min of LG-L, LG-LG and LG-H1 a bit higher, e.g. 0.25 or 0.3
>
> Increasing the min can not help, as I tested for another system.
>
> You know, the system has 4 beads LG (G)-H1(H)-L(L)-RG(G) ,inside parenthesis
> are the bead types. And the exclusion defined in cg-mapp.xml is as
> following:
>         <name>exclusion</name>
>         <beads>
>        LG RG
>         </beads>
>       </bond>
> And issue happens wherever LG is involved as I explained earlier.
>
> In a new system which has 5 beads as LG (G)-H1(H)-H2(H)-L(L)-RG(G), for
> which the exclusion defined in cg-mapp.xml is as following:
>        <name>exclusion</name>
>         <beads>
>        LG L
>        H1 RG
>         </beads>
>       </bond>
> Now, in the new system, addition to the LG, the problem also happen wherever
> H1 is involved.
> The point is that in both systems, the problem shows up for the beads types
> with more than one bead repetition. Like bead type G with LG and RG beads in
> the first system. And types G (beads LG and RG) and H (beads H1 and H2) in
> the second system.
> Don't you think somehow the portion of the repetitive bead is missing in
> calculations?
I am not sure what you mean, but you can always cross-check the
distribution calculation with gmx rdf.

>
> Another question: altering min/max ... in the settings.xml during simulation
> (for instance between step_n and step_n+1) causes crashing the job, so how
> to change them without starting a simulation from scratch?
I think you should be able to just remove the last (incomplete) step.
Otherwise, you just can use pot.new from the last step as a pot.in for
a new simulation from scratch.

Christoph

> Thank you.
> Regards,
> Alex
>>
>>
>> Christoph
>>
>> >
>> > Regards,
>> > Alex
>> >
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>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>
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-- 
Christoph Junghans
Web: http://www.compphys.de

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