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
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