normal Too many LINCS warning with ref-PW water

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1 month 1 week ago #8249 by bond_007
Hi,
I am using the refined polarizable water model (martini_v2.2refP.itp). During the NVT equil. phase I am using a 20fs timestep which then leads to too many LINCS warning where the bonds of the some PW beads rotate more than the allowed.

How do I solve this problem? The system I am simulation is a protein chain in solution. I used steepest descent for minimization and it seems like the system had converged to a min. energy, with the max. force on a protein bead in the order of ~100 .

There was a similar post about LINCS warning with the polarizable water model but the issue was not resolved.

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1 month 6 days ago #8256 by riccardo
Replied by riccardo on topic Too many LINCS warning with ref-PW water
Hi,
I think the last two posts in this other thread md.chem.rug.nl/index.php/component/kunen...ng-up-lincs-warnings can be helpful - if you haven't already tried what they suggest.
Also, I am not familiar with the refined PW, so not sure whether simulation settings may differ from the original PW?

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1 month 6 days ago #8257 by bond_007
Replied by bond_007 on topic Too many LINCS warning with ref-PW water
Hi riccardo,
Thanks for replying to me.

I have tried almost everything mentioned in the other thread. The only thing which works is that I have to use a reduced timestep of 10fs. This means that the water beads are under high forces, that lead to it violating the constraints, with a higher timestep. And I don't understand why the water molecules should be under the high forces after minimization. It would be really helpful if you could explain this.

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3 weeks 1 day ago #8281 by riccardo
Replied by riccardo on topic Too many LINCS warning with ref-PW water
As far as I know, the PW model should run also at 20 fs, but I am not really a user of the model. I am also not sure if anything changes with the ref-PW regarding recommended timestep or such - did you check if the authors say anything about it in the ref-PW publication?
A quick look at the itps tells me that they didn't change too much though..
Have you tried to replace the constraints with stiff bonds, i.e., use the commented out part of the itp:
; for minimization purposes replace constraints by stiff bonds:
;
;[bonds]
;  i     j   funct   length   force const.
;   1     2    1       0.14    50000
;   1     3    1       0.14    50000
during the minimization and then go back to constraints?

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