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

From: Bill Ross <>
Date: Wed, 2 Sep 2020 04:57:22 -0700

Looks like you can't do it with a GPU. I would be impressed if you could
do it on CPU. Imagine what would be coded: a rotating force on four
centers of mass, distributed to each atom, that would require lots and
lots of runtime to develop, and may not pay off. My bet having been to
Woodstock is that it hasn't been done.


On 9/2/20 4:18 AM, Akshay Prabhakant wrote:
> 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.
> Regards,
> Akshay Prabhakant.
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Received on Wed Sep 02 2020 - 05:00:02 PDT
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