[gmx-users] LINCS Constraints - all-bonds or h-bonds?

[Erik Marklund]

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.

Erik
 
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 
>> practice?
>> 
>> 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
>> 
>> -- 
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the 
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists