[AMBER] 列: Regarding dihedral scanning

From: Antonios Kolocouris <ankol.pharm.uoa.gr>
Date: Fri, 5 Jun 2015 12:51:35 +0300

is there any comparative benchmark in ns/day, for running amber MD of DHFR
all atoms (~24000 atoms) with GPU970 (1660 cores) and 980 (2048 cores)? I
mean to decide if there is a big difference between these cards on relative
efficiency in ns/day.

Antonios

-----榴鏖挈 燹眭灬-----
琉: Soumendranath Bhakat [mailto:bhakatsoumendranath.gmail.com]
琉矬麸朕: Friday, June 05, 2015 12:45 PM
旭矧: AMBER Mailing List
容灬: Re: [AMBER] Regarding dihedral scanning

Dear Daniel,

Can I add a print keyword to see the atom numbers which contributes in the
formation of phi or psi angles?

Thank you once again.

Best regards,
SB

On Thu, Jun 4, 2015 at 5:49 PM, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:

> Dear Daniel,
>
> You rock!! Thats exactly what I want. Got confused by seeing the
> scanning option.
>
> Tak
>
> /SB
>
> On Thu, Jun 4, 2015 at 5:30 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> On Thu, Jun 4, 2015 at 2:36 AM, Soumendranath Bhakat <
>> bhakatsoumendranath.gmail.com> wrote:
>>
>> > I wish to perform a dihedral scanning within A residues ranging
>> > from
>> 60-80
>> > within a beta-hairpin structure. I guess the dihedralscan keyword
>> > will
>> find
>> > all possible dihedrals within this residue range
>> >
>>
>> The 'dihedralscan' command is one of several poorly named commands in
>> cpptraj. As you can see from the online help and/or the manual, the
>> sole purpose of 'dihedralscan' is rotating dihedrals in intervals or
>> randomly (so perhaps the command name should be changed to
>> rotatedihedrals...). If what you want to do is calculate dihedral
>> angles in a certain residue range you want the 'multidihedral'
>> command, e.g.
>>
>> multidihedral MyDihedrals phi psi resrange 60-80 out PhiPsi-60-80.agr
>>
>> See the manual for full details on the command. Hope this helps,
>>
>> -Dan
>>
>>
>> >
>> > so I guess my input should be something like this
>> >
>> > trajin md_total.nc
>> > dihedralscan resrange :60-80 phi out dihedral.dat
>> >
>> > But is there any need of specifying the interval and random
>> > keywords in this case. Actually I partially understand the utility
>> > of these
>> keywords in
>> > scanning.
>> >
>> > I guess the interval keyword is necessary when we want to create a
>> > trajectory by rotating specified dihedrals in a structure by
>> > regular intervals but hence I just want to scan the trend of
>> > regular dihedrals I don't need to add the interval as well as random
keywords.
>> >
>> > Please let me know if I understand it correctly or there is any
mistake.
>> >
>> > Thanks in advance for your support.
>> >
>> > Regards,
>> > SB
>> >
>> > --
>> > Thanks & Regards;
>> > Soumendranath Bhakat
>> > Research Assistant, Division of Biophysical Chemistry, CMPS, Lund
>> > University, Sweden
>> > Homepgae: https://cbiores.wordpress.com/
>> > ResearchGate:
>> https://www.researchgate.net/profile/Soumendranath_Bhakat2
>> > Google Scholar:
>> > http://scholar.google.com/citations?user=Q1_nDMcAAAAJ&hl=en
>> > Past: Molecular Modelling and Drug Design Research Group Discipline
>> > of Pharmaceutical Sciences UKZN, Westville
>> > Weblink: http://soliman.ukzn.ac.za/Home.aspx
>> > and Department of Pharmaceutical Sciences Birla Institute of
>> > Technology, Mesra, India
>> > in.linkedin.com/pub/soumendranath-bhakat/15/79b/b9/
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Thanks & Regards;
> Soumendranath Bhakat
> Research Assistant, Division of Biophysical Chemistry, CMPS, Lund
> University, Sweden
> Homepgae: https://cbiores.wordpress.com/
> ResearchGate:
> https://www.researchgate.net/profile/Soumendranath_Bhakat2
> Google Scholar:
> http://scholar.google.com/citations?user=Q1_nDMcAAAAJ&hl=en
> Past: Molecular Modelling and Drug Design Research Group Discipline of
> Pharmaceutical Sciences UKZN, Westville
> Weblink: http://soliman.ukzn.ac.za/Home.aspx
> and Department of Pharmaceutical Sciences Birla Institute of
> Technology, Mesra, India
> in.linkedin.com/pub/soumendranath-bhakat/15/79b/b9/
>
>


--
Thanks & Regards;
Soumendranath Bhakat
Research Assistant, Division of Biophysical Chemistry, CMPS, Lund
University, Sweden
Homepgae: https://cbiores.wordpress.com/
ResearchGate: https://www.researchgate.net/profile/Soumendranath_Bhakat2
Google Scholar: http://scholar.google.com/citations?user=Q1_nDMcAAAAJ&hl=en
Past: Molecular Modelling and Drug Design Research Group Discipline of
Pharmaceutical Sciences UKZN, Westville
Weblink: http://soliman.ukzn.ac.za/Home.aspx
and Department of Pharmaceutical Sciences Birla Institute of Technology,
Mesra, India in.linkedin.com/pub/soumendranath-bhakat/15/79b/b9/
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Received on Fri Jun 05 2015 - 03:00:03 PDT
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