[gmx-users] virtual sites and heavy atoms for longer time steps

[Mark Abraham]

On 2/12/2010 11:13 AM, Hassan Shallal wrote:
> I have some issues to discuss with the mailing list users,
>
> 1- Is using virtual sites alone enough to allow me to lengthen the time step from 2 fs to 4 fs, or I have also to use heavy hydrogens when creating topology files in order to use 4 fs time step?
>
> 2- Another question, does vitual sites (assigning virtual hydrogens a mass of zero and adding their masses to the connected heavy atoms) opposes the effect of heavy atoms (increases the mass of the hydroen atoms) or vice versa.
> Or is the situation that heavy atoms treatment applies  when virtual sites treatment is not implemented, and we end up with a systme where some hydrogen atoms have no masses at all (those as virtual sites) whereas other hydrogen atoms are much heavier (those treated as heavy hydrogens)?
>
> 3- Implementing the scenario of some hydrogen atoms having zero masses and others having heavier masses, how would that affect the accuracy of predicting some energetic aspects like H-bonding? I know there is always a trade between efficiency or fastness and the accuracy because approximations usually fasten the job while decreasing the accuracy, but from experienced users point of view, how dangerous that approximation would be?
>
> Any answers or clarification of the above issues will be so much appreciated

Perhaps manual section 6.5 and ref therein will clarify some of this.

Mark