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, <[email protected]> wrote: Send gromacs.org_gmx-users mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of gromacs.org_gmx-users digest..." 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" <[email protected]> To: [email protected] Subject: [gmx-users] ultrasonic Message-ID: <[email protected]> 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" <[email protected]> To: [email protected] Subject: [gmx-users] ultrasonic Message-ID: <[email protected]> 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 <[email protected]> To: [email protected] Subject: [gmx-users] Exactly same rdfs for different residues of protein with water Message-ID: <CA+gTzoaZ0mj3t4vd3knUtFkK1JunaArFdQ-+72=gwxu5zh4...@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 <[email protected]> To: [email protected], [email protected] Subject: Re: [gmx-users] ultrasonic Message-ID: <camnumateupwa6r1nadj40vy5v2ekebwqvkza2znact7uftg...@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 <[email protected]> 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 [email protected]. > ------------------------------ Message: 5 Date: Sat, 17 Dec 2016 22:13:50 +0000 From: Mark Abraham <[email protected]> To: [email protected], [email protected] Subject: Re: [gmx-users] ultrasonic Message-ID: <camnumateupwa6r1nadj40vy5v2ekebwqvkza2znact7uftg...@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 <[email protected]> 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 [email protected]. > ------------------------------ Message: 6 Date: Sat, 17 Dec 2016 22:17:12 +0000 From: Mark Abraham <[email protected]> To: [email protected], [email protected] Subject: Re: [gmx-users] Exactly same rdfs for different residues of protein with water Message-ID: <camnumasf+fu_yfhsa_hbn2bmzn3chu62jgbecavk2vqsnft...@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 <[email protected]> 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 [email protected]. > ------------------------------ Message: 7 Date: Sat, 17 Dec 2016 22:17:12 +0000 From: Mark Abraham <[email protected]> To: [email protected], [email protected] Subject: Re: [gmx-users] Exactly same rdfs for different residues of protein with water Message-ID: <camnumasf+fu_yfhsa_hbn2bmzn3chu62jgbecavk2vqsnft...@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 <[email protected]> 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 [email protected]. > ------------------------------ -- 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 [email protected]. 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