Dear Debarati,
There is one more TI tutorial here
<
http://ambermd.org/tutorials/advanced/tutorial6/index.php>, this one is
for pKa (shift) calculations.
I'm trying to use the same with GPU (pmemd.cuda) but it gives the error
message that I mentioned in my first email in this thread.
I don't want atoms to disappear, but just change the charge distribution of
the existing cofactor.
http://ambermd.org/tutorials/advanced/tutorial6/index.php
Please let me know if you have any suggestions for doing this on GPU.
Thank you and best regards.
Vaibhav
On Wed, Oct 21, 2020 at 11:46 PM Debarati DasGupta <
debarati_dasgupta.hotmail.com> wrote:
> This is the only tutorial I found for TI runs. Please correct me if I am
> wrong.
> http://ambermd.org/tutorials/advanced/tutorial9/#setup_pmemd
>
> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
> From: Vaibhav Dixit<mailto:vaibhavadixit.gmail.com>
> Sent: 21 October 2020 09:00
> To: AMBER Mailing List<mailto:amber.ambermd.org>
> Subject: Re: [AMBER] TI not compatible with GB on GPU
>
> Dear Debarati,
> I think pmemd.MPI doesn't look like a correct usage, shouldn't it be
> pmemd.cuda.MPI? Moreover, it would apply only when the jobs are distributed
> between two GPU cards. That's what I interpreted from here
> <https://ambermd.org/GPUHowTo.php>.
> I have only one GPU card on this machine thus I was trying to run a single
> GPU job.
> It would be great if you can share your protocol (sample scripts and
> commands) in brief or share a tutorial that you are following.
>
> I'm estimating free energy of electron transfer (ET) and not protein-ligand
> binding free E, these ET free-Es are expected to between 95-110 kcal/mol.
> I'm assuming that the pKa shift tutorial is analogous to my case, they got
> ~55-60 kcal/mol free-Es and thus I'm trying similar simulations for my
> system which would be speeded up significantly on GPU. At present on HPC
> with 16 CPU-cores I'm getting only 0.17 ns/day which is very slow.
> Please let me know if you have an additional suggestion for me.
> I hope developers on the list will soon respond and give valuable
> suggestion on these TI simulations and their advantages/limitations and
> cautions to be kept in mind.
> Thank you and best regards.
> Vaibhav
>
>
>
>
> On Wed, Oct 21, 2020 at 5:52 PM Debarati DasGupta <
> debarati_dasgupta.hotmail.com> wrote:
>
> > 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<https://go.microsoft.com/fwlink/?LinkId=550986> for
> > Windows 10
> >
> > 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,
> > ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> > 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
> >
> > P Please consider the environment before printing this e-mail
> > _______________________________________________
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> >
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
>
> 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,
> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> 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
>
> P Please consider the environment before printing this e-mail
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
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
P Please consider the environment before printing this e-mail
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Received on Thu Oct 22 2020 - 03:30:02 PDT
