Re: [AMBER] GPU based TI runs

From: Debarati DasGupta <>
Date: Sat, 9 May 2020 14:00:52 +0000

Hello Prof Case,
I have used barostat=2 (MC barostat) in my input files but I have not been able to still do the NPT equilibration on the GPUs using pmemd.cuda

I am using the cpu processors for NPT (ns) equilibration, as I could not figure out the technique to do it on GPUs, but my project will probably go on for 6 months more before I can see any data produced. On cpus (16 processors) I am getting 0.6ns/day whereas my minimization/heating on GPUs were so fast at all the 12 lambdas. ( Another interesting thing I discovered was that sometimes when I keep restarting the equil runs on GPUs, some lambda values get output produced and immediately after 2-3mins of initiation of the job; my job crashes...)

50000Steps of SD and 100ps(0-50K), 100ps(50-100K), 100ps(100-200K),100 ps(200-300K), 100ps(300K) -----> these steps all together took like 1.8 hours on the GPU.
Now I m struggling with 40+ hours of NPT equilibration.
I have not heard from Dr Cerutti yet; I am hoping he may have some ideas which can help me push the 2ns of equilibration on gpuland.

Thanks Prof Case for all your inputs on my TI simulations.


From: David A Case<>
Sent: 09 May 2020 09:10
To: AMBER Mailing List<>
Cc: Dave Cerutti<>
Subject: Re: [AMBER] GPU based TI runs

On Sat, May 09, 2020, Debarati DasGupta wrote:
>Is there anyone here on the mailing list who has done extensive absolute
>free energy TI calculations; specifically :NPT equilibrations on GPUs and
>have seen success?

>This is in reference to Thermodynamic integration calculations on AMBER18.
>Well, I have been working on it last ~5-6 months and it seems and
>whatever I try, the 2ns of density equilibration (ntp=1) ALWAYS fails on
>the GPUs.

Do you see any different behavior when using the Monte Carlo barostat?

Generally, people doing free energy TI calculations don't post much to
this email list, and I suspect that they don't follow it. Dave Cerutti
was supposed to be working on this (as I remember...could be getting
different threads mixed up here.) I'll cc- him here.


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Received on Sat May 09 2020 - 07:30:02 PDT
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