You can use plumed, as long as you are scaling all of your protein (as
you would be with REST2). You just need to post-process the output of
the plumed partial_tempering script:
https://groups.google.com/d/msg/plumed-users/lo-Sb8aUepY/X54UEB-tAgAJ
https://groups.google.com/d/msg/plumed-users/Txlf8Icwr2k/71wHv7lh1lAJ
Cheers
Tom
On 10/01/2019 17:05, Aram Davtyan wrote:
Hello dear users,
I am trying to figure out how to run Replica Exchange with Solute Tempering
(REST2) simulation using CHARMM 36m force filed. The only method that I
found so far involves using Plumed (which would have worked for me).
However, the instructions I found (
https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplumed.github.io%2Fdoc-v2.4%2Fuser-doc%2Fhtml%2Fhrex.html&data=01%7C01%7Ct.piggot%40soton.ac.uk%7C37ba206a42b04e9e692e08d6771e03d5%7C4a5378f929f44d3ebe89669d03ada9d8%7C1&sdata=7x7kT8kS%2BTF5Z90C%2FwoGQJhPpYbyrs1%2BtrS4SlxtxE8%3D&reserved=0)
explicitly say
that it will not work with CHARMM cmap. Thus, I was wondering if anyone
knows an alternative method of run REST2 simulations in GROMACS in general
or how to solve the cmap problem mentioned in the instructions.
Thank you in advance,
Aram
--
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.
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