Re: [AMBER-Developers] New Year fixes for Amber

From: Ross Walker <>
Date: Mon, 06 Jan 2014 17:12:02 -0800

I am copying in Romelia here since it seems the email she had registered
for the developers list has 'expired'. Romelia can confirm for sure but I
believe that the current situation with regards to SGLD is that it is done
in the CPU code but there is no GPU version of it. This is likely how it
will get released unless we magically find time to add it to the GPU code
before the code freeze. It likely still needs to be documented though.

All the best

On 1/3/14 12:21 PM, "Wu, Xiongwu (NIH/NHLBI) [E]" <>

>Hi Jason,
>Thanks for the information. I will work based on Scott's SGLD branch.
>Romelia, it would be very helpful if you have an implementation to share.
>> -----Original Message-----
>> From: Jason Swails []
>> Sent: Friday, January 03, 2014 1:14 PM
>> To:
>> Subject: Re: [AMBER-Developers] New Year fixes for Amber
>> On Fri, 2014-01-03 at 12:23 -0500, David A Case wrote:
>> > On Fri, Jan 03, 2014, Wu, Xiongwu (NIH/NHLBI) [E] wrote:
>> >
>> > > I will implement SGLD to pmemd and pmemd.cuda if no one else is
>> doing it.
>> > > Thanks and see you at the Amber meeting.
>> >
>> > Thanks!...note that there is a very beginning (look for "ifdef SGLD")
>> in
>> > $AMBERHOME/src/pmemd/src.
>> To add on to this a little, I know Scott Brozell started to work on
>> that
>> while he was at Rutgers awhile ago. He started a branch (sgld) which
>> he
>> pushed to the main git repo, and it may be a better starting point
>> (unless master cannot be easily merged, then it may be worth starting
>> over).
>> IIRC, though, he stopped after he was informed that Romelia from Ross's
>> lab was working on the implementation. I'm not sure where we are with
>> this now, but it may be worth coordinating efforts.
>> All the best,
>> Jason
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER-Developers mailing list
>AMBER-Developers mailing list

AMBER-Developers mailing list
Received on Mon Jan 06 2014 - 17:30:03 PST
Custom Search