normal Polarized W

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5 years 11 months ago #1677 by dariush
Polarized W was created by dariush
Hi,

In the MARTINI website, it has been explained convert normal water to PW.
I am wondering to know can I directly use genbox?
genbox -cp mol.gro -cs PW.gro -vdwd 0.21 -o out.gro

I tried minimize this out.gro file, but I got error (lincs warning). I have "constraint:none".
What can be the problem?
Is there any template for minimize the system having protein+PW+lipids?

Thanks,
Dariush

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5 years 11 months ago #1678 by djurre
Replied by djurre on topic Polarized W
In principle this should work, however we have seen previously that this gives sometimes problems (for example the LINCS warnings you mention).

Therefore, in my experience, it is easier to solvate it with normal water and convert that to polarizable water. If that doesn't work directly you could even energy minimize/run the normal water for a bit and then convert it to polarizable water.

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5 years 11 months ago #1682 by xavier
Replied by xavier on topic Polarized W
You also have to be careful what and ow you solvate it.

It is not clear how and what you solvate!

djurre wrote: In principle this should work, however we have seen previously that this gives sometimes problems (for example the LINCS warnings you mention).

Therefore, in my experience, it is easier to solvate it with normal water and convert that to polarizable water. If that doesn't work directly you could even energy minimize/run the normal water for a bit and then convert it to polarizable water.

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