[gmx-users] Implicit Solvent and Box Size

[Paul bauer]

Hello,

the implicit solvent functionality has been deprecated a while ago in 
GROMACS and has been removed in the recent versions.

Can the simulations also be run in explicit solvents (that are a better 
physical representation anyway)?

Cheers

Paul

On 07/10/2019 16:50, 张 卓 wrote:
> Hi, I am doing the aggregations of small peptides in implicit solvents. However, it seems that there is no detailed tutorial on such subject and I just turned on the 'implicit solvent' option in the .mdp file. However, I found that the box was compressed during mdrun. It comes to me that the implicit solvent is only a field rather than some virtual material. I believe that the compression should be due to pressure coupling.  Then should I use NPT ensemble for implicit solvents. If so, how can I keep the box size with pressure coupling?
>
>
> Thanks for your help!
>
>
> Regards,
>
> Zhuo


-- 
Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594