DId you try to use it in pmemd?
adrian
________________________________________
From: Sajeewa Pemasinghe [sajeewasp.gmail.com]
Sent: Wednesday, November 07, 2012 2:30 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Umbrella sampling with pmemd
Hi Dr.Roitberg,
Well in section 4.2 (umbrella sampling) in amber11, amber12 manuals there
is no mentioning of anything about pmemd. When I check the section 7.2
(functionality of pmemd) it says nmrpot=2 is NOT supported but doesn't say
anything about supporting or not supporting nmropt=1 with harmonic
constraints.
This page
http://www.uky.edu/ukit/hpc/docs/Amber/v12-new-features says
"Additional
features from Sander have been added to the pmemd code for both CPUs and
GPUs, including Temperature Replica Exchange, Isotropic Periodic Sum,
Accelerated Molecular Dynamics and support for various harmonic restraints
based on the use of NMRopt on GPUs".
But I am NOT using GPUs. So as it is quite vague I just needed a straight
answer from you guys. As of now I think umbrella sampling is NOT supported
but just want to be more sure.
Sajeewa Dewage
On Wed, Nov 7, 2012 at 2:03 AM, Roitberg,Adrian E <roitberg.ufl.edu> wrote:
> Hi
>
> did you try to read the manual or run the calculation ?
>
> I would do that before asking the list....
>
> adrian
>
> ________________________________________
> From: Sajeewa Pemasinghe [sajeewasp.gmail.com]
> Sent: Wednesday, November 07, 2012 1:59 AM
> To: AMBER Mailing List
> Subject: [AMBER] Umbrella sampling with pmemd
>
> Hi all,
>
> I am going to do umbrella sampling. My restraints are of the form
>
> &rst iat=15360,15377, r1=0.0, r2=11.8, r3=11.8, r4=100.0, rk2 = 30.0, rk3
> = 30.0, /
>
> where r2/r3 have been specified as the Cartesian distance between the two
> atoms specified by iat. Does PMEMD support umbrella sampling with this kind
> of constraints?
>
> Thank you
>
> Sajeewa Dewage
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Received on Wed Nov 07 2012 - 07:30:03 PST
