Dear Amber users,
I understand that the larger is the cutoff for nonbonded interactions
("cut" parameter) the better, however, larger values dramatically slows
down the calculations. So its really the question of what resources you
have. Since the computer power gets more affordable every year I assume
that the "normal" cutoff, i.e. what users typically set to make their
simulations supposedly more realistic, also increases. So my aim is to
understand the current "normal" average.
I myself use Tesla K40s accelerators. I set the cut=12 and then make
water box with at least 15A gap between the protein and the cell edges
(to avoid situations when the protein interacts with itself from another
cell). With these settings four GPU units provide an average speed of
approximately 8-40 ns/day for systems of 190 000 - 70 000 atoms,
respectively (in NVT). Using more units does not improve the
performance, so this is the maximum I can get. This speed is comfortable
for my tasks and so I stick with these settings.
How do you set you cutoff and box gap? Would you use a larger cut if you
could?
Thanks for your time
Dmitry
On 08/18/2016 10:00 PM, amber-request.ambermd.org wrote:
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> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Problem when visualizing bonds in VMD (Xiaoliu Zhang)
> 2. Re: Problem when visualizing bonds in VMD (Jason Swails)
> 3. Re: Is there any CG martini parameter for K+? (Pengfei Li)
> 4. QM region has an odd number of electrons (Corum, Katharine W)
> 5. Re: QM region has an odd number of electrons
> (Dr. Andreas W. Goetz)
> 6. RMSd (Wong Li Zhe)
> 7. Re: RMSd (Hai Nguyen)
> 8. Re: RMSd (Wong Li Zhe)
> 9. Re: RMSd (Wong Li Zhe)
> 10. Re: MD simulation with non natural amino acid, parameterized
> using the RED server (Cecilia Lindgren)
> 11. Re: RMSd (Bill Ross)
> 12. Re: MD simulation with non natural amino acid, parameterized
> using the RED server (Bill Ross)
> 13. Re: solid surface simulation in amber (Neha Gandhi)
> 14. Re: solid surface simulation in amber (Bill Ross)
> 15. Re: MD simulation with non natural amino acid, parameterized
> using the RED server (Cecilia Lindgren)
> 16. Re: solid surface simulation in amber (Neha Gandhi)
> 17. Re: MD simulation with non natural amino acid, parameterized
> using the RED server (Bill Ross)
> 18. LEaP and PARMSETs (Aronica, Pietro)
> 19. Re: solid surface simulation in amber (Bill Ross)
> 20. Re: MD simulation with non natural amino acid, parameterized
> using the RED server (Cecilia Lindgren)
> 21. Re: MD simulation with non natural amino acid, parameterized
> using the RED server (Bill Ross)
> 22. Re: MD simulation with non natural amino acid, parameterized
> using the RED server (Hannes Loeffler)
> 23. a bug in leaprc.gaff2 file (Ye Mei)
> 24. Re: MD simulation with non natural amino acid, parameterized
> using the RED server (Bill Ross)
> 25. Re: MD simulation with non natural amino acid, parameterized
> using the RED server (Cecilia Lindgren)
> 26. Re: [AMBER} NetCDF installation problem on mac OS X El
> Capitan (Jason Swails)
> 27. Re: solid surface simulation in amber (David A Case)
> 28. Re: a bug in leaprc.gaff2 file (David A Case)
> 29. Re: a bug in leaprc.gaff2 file (David A Case)
> 30. Problem in charge generation through antechamber (ATUL KUMAR)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 17 Aug 2016 19:40:22 +0000
> From: Xiaoliu Zhang <xzhan91.lsu.edu>
> Subject: [AMBER] Problem when visualizing bonds in VMD
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID:
> <BY1PR0601MB133393B49EDBEFFBD1EBE94CA7140.BY1PR0601MB1333.namprd06.prod.outlook.com>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Amber users,
>
>
> I'm using amber with Amoeba force field following the Amber 16 manual, chapter 17.
>
>
> After I got prmtop and inpcrd file by using tinker_to_amber command, I tried VMD to visualize my molecule. My Ambertool is 16 version and VMD is 1.9.1.
>
>
> First i got an error:
>
> AMBER 7 parm read error at flag section TITILE.
>
> expected format %FORMAT(20a4) but got %FORMAT(a)
>
>
> Then, I checked my topology file and found that it begins with this:
>
>
> %VERSION VERSION_STAMP = V0001.000 DATE = 08/17/16 08:18:25
> %FLAG TITLE
> %FORMAT(a)
> 7box_5 ameoba FF
> %FLAG POINTERS
> %FORMAT(10I8)
>
> I changed the %FORMAT(a) to %FORMAT(20a4) by hand and ran again.
>
>
> This time there's no error in terminal. However, no matter I choose VDW or CPK, there are only atoms showing on the screen, not any bond information at all.
>
>
> Do you know how to fix this problem?
>
>
> Thanks in advance.
>
>
> Xiaoliu
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 17 Aug 2016 16:17:27 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] Problem when visualizing bonds in VMD
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3r8uYSuqwK3=hpfdsrD457wqbJcZ0cBGy_mq=H9-bEQxA.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Wed, Aug 17, 2016 at 3:40 PM, Xiaoliu Zhang <xzhan91.lsu.edu> wrote:
>
>> Dear Amber users,
>>
>>
>> I'm using amber with Amoeba force field following the Amber 16 manual,
>> chapter 17.
>>
>>
>> After I got prmtop and inpcrd file by using tinker_to_amber command, I
>> tried VMD to visualize my molecule. My Ambertool is 16 version and VMD is
>> 1.9.1.
>>
>>
>> First i got an error:
>>
>> AMBER 7 parm read error at flag section TITILE.
>>
>> expected format %FORMAT(20a4) but got %FORMAT(a)
>>
>>
>> Then, I checked my topology file and found that it begins with this:
>>
>>
>> %VERSION VERSION_STAMP = V0001.000 DATE = 08/17/16 08:18:25
>> %FLAG TITLE
>> %FORMAT(a)
>> 7box_5 ameoba FF
>> %FLAG POINTERS
>> %FORMAT(10I8)
>>
>> I changed the %FORMAT(a) to %FORMAT(20a4) by hand and ran again.
>>
>>
>> This time there's no error in terminal. However, no matter I choose VDW
>> or CPK, there are only atoms showing on the screen, not any bond
>> information at all.
>>
>>
>> Do you know how to fix this problem?
>>
> ?You can't use AMOEBA topology files with VMD easily.
>
> Try using a PDB as the topology instead.
>
> HTH,
> Jason
>
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Received on Fri Aug 19 2016 - 05:00:02 PDT
