[gmx-users] A special case of cutoffs related to mdrun with -rerun option

[Mark Abraham]

On 3/12/2011 2:02 AM, Ioannis Beis wrote:
> Dear GROMACS users,
>
> I am interested in using mdrun of a special version of GROMACS 4.0.2 
> made by Ollila et. al with -rerun option, made so that it can allow 
> calculations of properties related to local pressure in lipid bilayer 
> systems. I have used GROMOS54a7 with Poger parameters, but among other 
> slight modifications I have used PME instead of reaction field with 
> rcoulomb=0.9 and maintained the twin range cutoff used in the original 
> study for van der Waals, using rlist=0.9 (instead of the original 0.8) 
> and rvdw=1.4. The inner sphere neighborlist is updated every step, 
> whereas the outer sector neighborlist every 5 steps.
>
> The mdrun with -rerun flag of this package does not support PME, 
> therefore the tpr file has to be reassembled without it. Instead, much 
> larger plain cutoff than 1.8 alone has been shown by Sonne et al. to 
> give close enough results to short cutoffs used together with PME, at 
> least in a qualitative manner.
>
> I can thereby use rcoulomb=2.0 for the purposes of the -rerun, but 
> this no longer allows the twin range cutoff scheme. I tried to check 
> if there could be some trick to be done with rlistlong (although I was 
> almost sure there wouldn't be anything and that rlistlong just serves 
> for switch/shift functions), but as far as my searching is concerned 
> it didn't even exist as an option in GROMACS 4.0.2 (I assume that twin 
> range cutoff was still supported but rlistlong would be automatically 
> placed in the max(rcoulomb,rvdw).
>
> Therefore my current problem is about the reliability of -rerun with 
> plain vdw cutoff, while in the original simulation twin range cutoff 
> was used. Is there any study comparing the results of the two 
> different schemes mentioned above for GROMOS simulations? What would 
> the consequenses in the physics be and how would the choice of the 
> cutoff radius and number of steps affect the results? If someone 
> really wants to obtain those calculations, what would be the best 
> compromise?

VDW potentials are very close to zero by 0.9nm, so I'd expect you can do 
whatever you like here. Off the cuff, I'd be far more concerned about 
Coulomb cut-off force artefacts from plain (or RF) cut-offs, even out at 
2nm, but do graph the potentials and see.

Mark

>
> If anyone has another recommendation about obtaining lateral presure 
> profiles and associated properties by lipid bilayer simulations, such 
> that would be compatible with my algorithm choices, please let me know.
>
> I am grateful in advance.
>
> Best regards,
> Ioannis
>