Hi Vaibhav,
Welcome to the TI club!
I feel on GPUs, you should be using pmemd.MPI not pmemd.cuda as I have used pmemd.MPI while running my TI jobs.
Also I am not sure what is the exact system your studying as 100-150 kcal/mol looks like a very very high energy binding process.
I have some weak binders I work on and my free energies are in the range of -1 to -3 kcal/mol for binding to my kinase.
Also the Amber20 TI-GPU is pretty fast. On a single GPU, I get about ~70ns/day in equilibration stages.
I am not sure if we could use implicit solvents for TI, I have been using TIP3P water.
Thanks
I hope I could help somewhat.
Debarati
Sent from Mail<
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From: Vaibhav Dixit<mailto:vaibhavadixit.gmail.com>
Sent: 20 October 2020 09:02
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: [AMBER] TI not compatible with GB on GPU
Dear Amber users/experts,
I'm running at TI calculation on CPU but it is expected to take 353 hr to
complete.
When I tried to run the same on GPU with pmemd.cuda I'm getting hte subject
error mentioned below.
Can someone on the list please guide me if there is a way around this or is
it not possible with Amber18 on GPU?
Additionally, I was expecting free energy values in the range 100-115
kcal/mol, but I'm getting 180 kcal/mol values. I did run a 30 ns
simulation on the model compound but values did not change much. I used
procedure similar to that given in the tutorial here
<
http://ambermd.org/tutorials/advanced/tutorial6/section4.php>. My system
is Heme with and without extra electron, charges were derived from MCPB.py
tool.
We are processing the purchase of Amber20, but it might take 15-20 days or
more before the payment goes through. Is this something available in
Amber20?
thank you and best regards.
Error while running GB based TI on GPU
Note: ig = -1. Setting random seed to 390103 based on wallclock time in
microseconds.
| irandom = 1, using AMBER's internal random number generator (default).
| ERROR: TI is incompatible with GB on GPU
Input errors occurred. Terminating execution.
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
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Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Wed Oct 21 2020 - 05:30:02 PDT
