[gmx-users] LINCS Constraints - all-bonds or h-bonds?
erikm at xray.bmc.uu.se
Fri Aug 16 15:26:51 CEST 2013
I often use 4 fs with all-bonds and virtual sites, especially if lacking sampling is a greater source of error than the kinetic energy being slightly off.
On 15 Aug 2013, at 20:58, Michael Shirts <mrshirts at gmail.com> wrote:
> I don't go beyond 2 fs with either all- bonds or h-bonds. Things like kinetic energy start being subtly off.
> H-bonds has less chance of failing with large numbers of constraints- less iteration required, especially if bond system cross parallelization boundaries.
> If your molecules are < 10 atoms, it probably doesn't matter either way.
> Sent from my iPhone
> On Aug 15, 2013, at 9:11, "Barnett, James W." <jbarnet4 at tulane.edu> wrote:
>> Searching through this mailing list it seems like some have stated that
>> with a 2 fs timestep (dt=0.002), constraints=h-bonds is fine in general.
>> The questions I have are:
>> 1) What are some personal opinions on when it is ok to switch to h-bonds
>> from all-bonds for LINCS constraints? Is 2 fs and h-bonds a general
>> 2) Also, if typically 2 fs and h-bonds are ok, what time-step do users
>> (or you personally) generally go to with all-bonds?
>> I am speaking generally here of course. Thanks for your responses.
>> Wes Barnett | jbarnet4 at tulane.edu
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