[gmx-users] exactly same rdfs for different residues
Apramita Chand
apramita.chand at gmail.com
Sun Dec 18 05:21:23 CET 2016
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>
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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!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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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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