[gmx-users] exactly same rdfs for different residues

Sun Dec 18 05:41:44 CET 2016

Hi,

That sounds all correct, but you can double check which atom indices are in
the ndx file. It seems wildly improbable that different indices can produce
the same numerical result.

Mark

On Sun, 18 Dec 2016 15:21 Apramita Chand <apramita.chand at gmail.com> wrote:

> Dear All,
> Thank you Mark,for your reply.The rdfs not only look the same,they have
> same computed values in the xvg files.For example,the oxygen of methionine
> and oxygen of tyrosine and oxygen of glycine etc rdfs with hydrogen of
> water come exactly same and coincide.
> I have double checked the index numbers. I created a single index file
> containing all the atoms of different residues and solvent. I named them
> differently. I chose 'a O r1', 'a O r2' etc while creating index file and
> the names were distinct like O_r1,O_r2.
> Is it a problem that I used the same index file? In the command line
> though, I choose O_r1 first then HW and in a similar way, I have generated
> different rdfs.
> Should I create different index files? Please suggest the proper way.
>
> Regards,
> Apramita
>
> On Dec 18, 2016 3:48 AM, <
> gromacs.org_gmx-users-request at maillist.sys.kth.se>
> wrote:
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> Today's Topics:
>
>    1. ultrasonic (aghaei.arsalan)
>    2. ultrasonic (aghaei.arsalan)
>    3. Exactly same rdfs for different residues of protein       with
>       water (Apramita Chand)
>    4. Re: ultrasonic (Mark Abraham)
>    5. Re: ultrasonic (Mark Abraham)
>    6. Re: Exactly same rdfs for different residues of protein with
>       water (Mark Abraham)
>    7. Re: Exactly same rdfs for different residues of protein with
>       water (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 17 Dec 2016 14:55:05 +0330
> From: "aghaei.arsalan" <aghaei.arsalan at ut.ac.ir>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] ultrasonic
> Message-ID: <0a7135d42331cfca96c695259234f892 at ut.ac.ir>
> Content-Type: text/plain; charset=US-ASCII
>
> Dear Justin
>
> how can ultrasonic sound wave be introduced in simulation using
> Gromacs.?
>
> i am looking forward to hear from you
>
> Best Regards
>
>  _Arsalan Aghaei_
> _    PhD Student in Biophysics_
> _    Institute of Biochemistry and Biophysics_
> _    University of Tehran_
> _    www.ibb.ut.ac.ir [1]_
>
> Links:
> ------
> [1] http://www.ibb.ut.ac.ir/
>
> ------------------------------
>
> Message: 2
> Date: Sat, 17 Dec 2016 17:08:04 +0330
> From: "aghaei.arsalan" <aghaei.arsalan at ut.ac.ir>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] ultrasonic
> Message-ID: <214badae14fad44e7d9e4193abf9ffe6 at ut.ac.ir>
> Content-Type: text/plain; charset=US-ASCII
>
> Dear Sir/Madam
>
> I want to do a simulation using Gromacs by applying ultrasonic treatment
> on my protein.
>
> does anybody know how to introduce ultrasonic sound wave in MD
> simulation input files?
>
> Best Regards
>
> ------------------------------
>
> Message: 3
> Date: Sat, 17 Dec 2016 20:35:25 +0530
> From: Apramita Chand <apramita.chand at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Exactly same rdfs for different residues of
>         protein with water
> Message-ID:
>         <CA+gTzoaZ0mj3t4vd3knUtFkK1JunaArFdQ-+72=
> GWXu5zH4FXg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear All,
>  I'm trying to see how the rdf varies for a particular interaction (peptide
> carbonyl oxygen with hydrogen of water) across different residues. I chose
> the oxygen atoms belonging to different residues in the index file and also
> chose the hydrogen atoms from water. To my surprise, all the rdfs for
> different residues are exactly coinciding with each other. I checked with
> both corrected and uncorrected trajectory files. Also, I checked with
> another simulation, where I've made a binary mixture. In that simulation,
> this particular interaction again coincides exactly . When I plot both
> files from these two simulations , two different plots (corresponding to
> all coincided rdfs from different residues for each simulation) are seen.
> Can anyone please explain this anomaly?
>
> Regards,
> Apramita
>
>
> ------------------------------
>
> Message: 4
> Date: Sat, 17 Dec 2016 22:13:50 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] ultrasonic
> Message-ID:
>         <
> CAMNuMATeUPwA6r1NADj40vY5v2eKebWQvkZA2ZnAct7uFtGT2A at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> You'd have to produce a series of alternating compressions and
> rarefactions, but there's no code that generates that. You'd also have to
> consider whether you can simulate enough particles to get to observe the
> behaviour in bulk matter.
>
> Mark
>
> On Sun, Dec 18, 2016 at 12:38 AM aghaei.arsalan <aghaei.arsalan at ut.ac.ir>
> wrote:
>
> > Dear Sir/Madam
> >
> > I want to do a simulation using Gromacs by applying ultrasonic treatment
> > on my protein.
> >
> > does anybody know how to introduce ultrasonic sound wave in MD
> > simulation input files?
> >
> > Best Regards
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 5
> Date: Sat, 17 Dec 2016 22:13:50 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] ultrasonic
> Message-ID:
>         <
> CAMNuMATeUPwA6r1NADj40vY5v2eKebWQvkZA2ZnAct7uFtGT2A at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> You'd have to produce a series of alternating compressions and
> rarefactions, but there's no code that generates that. You'd also have to
> consider whether you can simulate enough particles to get to observe the
> behaviour in bulk matter.
>
> Mark
>
> On Sun, Dec 18, 2016 at 12:38 AM aghaei.arsalan <aghaei.arsalan at ut.ac.ir>
> wrote:
>
> > Dear Sir/Madam
> >
> > I want to do a simulation using Gromacs by applying ultrasonic treatment
> > on my protein.
> >
> > does anybody know how to introduce ultrasonic sound wave in MD
> > simulation input files?
> >
> > Best Regards
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 6
> Date: Sat, 17 Dec 2016 22:17:12 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Exactly same rdfs for different residues of
>         protein with water
> Message-ID:
>         <
> CAMNuMASF+FU_yfhsA_HBN2BmZn3ChU62JgbEcaVk2VqSNfTu-w at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> If "exactly coinciding" means the same numbers are computed in the .xvg
> file, then you probably are just computing the same thing each time -
> double check your index groups and command-line choices. If you mean that
> they just look the same, then that could be a fair result if your protein
> is small - you only expect differences at very short ranges, after all.
>
> Mark
>
> On Sun, Dec 18, 2016 at 2:05 AM Apramita Chand <apramita.chand at gmail.com>
> wrote:
>
> > Dear All,
> >  I'm trying to see how the rdf varies for a particular interaction
> (peptide
> > carbonyl oxygen with hydrogen of water) across different residues. I
> chose
> > the oxygen atoms belonging to different residues in the index file and
> also
> > chose the hydrogen atoms from water. To my surprise, all the rdfs for
> > different residues are exactly coinciding with each other. I checked with
> > both corrected and uncorrected trajectory files. Also, I checked with
> > another simulation, where I've made a binary mixture. In that simulation,
> > this particular interaction again coincides exactly . When I plot both
> > files from these two simulations , two different plots (corresponding to
> > all coincided rdfs from different residues for each simulation) are seen.
> > Can anyone please explain this anomaly?
> >
> > Regards,
> > Apramita
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 7
> Date: Sat, 17 Dec 2016 22:17:12 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Exactly same rdfs for different residues of
>         protein with water
> Message-ID:
>         <
> CAMNuMASF+FU_yfhsA_HBN2BmZn3ChU62JgbEcaVk2VqSNfTu-w at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> If "exactly coinciding" means the same numbers are computed in the .xvg
> file, then you probably are just computing the same thing each time -
> double check your index groups and command-line choices. If you mean that
> they just look the same, then that could be a fair result if your protein
> is small - you only expect differences at very short ranges, after all.
>
> Mark
>
> On Sun, Dec 18, 2016 at 2:05 AM Apramita Chand <apramita.chand at gmail.com>
> wrote:
>
> > Dear All,
> >  I'm trying to see how the rdf varies for a particular interaction
> (peptide
> > carbonyl oxygen with hydrogen of water) across different residues. I
> chose
> > the oxygen atoms belonging to different residues in the index file and
> also
> > chose the hydrogen atoms from water. To my surprise, all the rdfs for
> > different residues are exactly coinciding with each other. I checked with
> > both corrected and uncorrected trajectory files. Also, I checked with
> > another simulation, where I've made a binary mixture. In that simulation,
> > this particular interaction again coincides exactly . When I plot both
> > files from these two simulations , two different plots (corresponding to
> > all coincided rdfs from different residues for each simulation) are seen.
> > Can anyone please explain this anomaly?
> >
> > Regards,
> > Apramita
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
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