[AMBER] best way to umbrella-sample a pseudo-dihedral angle Collective Variable

From: Akshay Prabhakant <akshayresearch16.gmail.com>
Date: Wed, 2 Sep 2020 16:48:17 +0530

A warm hello to the AMBER community,
I would like to ask everyone the best way to carry out an umbrella-sampling
simulation for a pseudo-dihedral angle(COM's of 4 groups as specified by me
will be treated as the 4 points used to calculate the dihedral angle) as a
collective variable, using pmemd(and not sander, since my system is
large(more than 100K atoms), and hence won't be able to maintain such a
time-wise lengthy simulation). I have already eliminated the nmropt method
and plumed, since I found out that there is no support for PLUMED in pmemd,
and for nmropt=1 type of umbrella sampling simulations, "Implementation
does not currently support the use of COM simulations for angle or dihedral
restraints. Require iat(3) >= 0 " was encountered. I have attached a
screenshot for the same.

[image: Screenshot from 2020-09-01 18-36-04.png]

Thank You in advance.

Akshay Prabhakant.

AMBER mailing list

(image/png attachment: Screenshot_from_2020-09-01__18-36-04.png)

Received on Wed Sep 02 2020 - 04:30:02 PDT
Custom Search