Date: Wed, 04 Aug 2010 00:23:34 +0200
Dear Bill,
First of all thank you very much for your response !
Regarding to degradation of the surface structure please see attached
pictures, I hope that there is everything clearly seen.
The surface block is initially placed so close to the box edge because
it was solvated with minimal distance of the box side from solute only 5A
(solvatebox name TIP3PBOX 5) in this case.
Why the surface (and also whole simul. box) so increased it's volume is
mystery also for me.
The temperature is 373K but the pressure is 20 atmospheres, moreover the
same problem I obtained in simulation under pressure 80 atmospheres.
I would maybe suppose small shrinkage of the system which is by default
probably set to "normal conditions" (initial water density).
Anyway I also attached relevant *.out files.
It seems that the main problem here is with pressure regulation (see the
average RMS fluctuations in prod_HA_PU.out). Also the target pressure was
not achieved (30 atm. instead desired 20)
I will try to play a little with relevant parameters like "taup", I will
also try to confirm that the problem is probably with press reg. using
NVT simul. instead
NPT and also I will experiment with the harmonic RESTRAINT instead ibelly
CONSTRAINT.
Anyway if anybody already solved at least the problem with "fixing" of
the solid surface during NPT simul.
please let me know to save me from wasting much time with such kind of
"experiments".
Best wishes,
Marek
>
> Dne Tue, 03 Aug 2010 21:14:57 +0200 Bill Ross <ross.cgl.ucsf.edu>
> napsal/-a:
>
>> The surface simulation issue has come up enough that I think it's
>> worth having some way of keeping the surface parallel to the box side,
>> e.g. by having an option not to reorient the solute on principal axes
>> before placing the box, also maybe to not add buffer in half of one
>> axis.
>>
>> One approach would be to allow the user to draw the box in xleap,
>> then have it filled in with water.
>>
>> The expanded surface still looks ordered. You could also try adding
>> Cartesian restraints instead of belly to allow a little movement, but
>> there's no reason to think it would affect the structural change. The
>> interesting questions to me are why the surface block is initially
>> placed so close to the box edge, and why box grows.
>>
>> Bill
>>
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>>
>
>
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- application/zip attachment: OUT_files.zip
(image/jpeg attachment: HA_End_01.jpg)
(image/jpeg attachment: HA_End_02.jpg)
(image/jpeg attachment: HA_Start_01.jpg)
(image/jpeg attachment: HA_Start_02.jpg)
