Re: [gmx-users] Regarding calculation of angles

2017-04-09 Thread Justin Lemkul
On 4/9/17 12:27 PM, Dilip H N wrote: Suppose for eg., in glycine how can i calculate the angle between nitrogen and hydrogen attached to it, angle between C alpha and H alpha etc., You can't calculate the angle between two angles; you need at least three. Regardless, you can easily just

Re: [gmx-users] Regarding calculation of angles

2017-04-09 Thread Dilip H N
9, 2017 at 9:49 PM, Dilip H N <cy16f01.di...@nitk.edu.in> wrote: > Hello, > I have ran a amino acid simulation, and i want to calculate the angle > between the atoms in amino acid molecule. how can i calculate it..?? > > gmx angle [-f [<.xtc/.trr/...>]] [-n [<.ndx>]

[gmx-users] Regarding Cos theta functions calculations in gromacs...

2017-04-13 Thread Dilip H N
is it calculating two angles θ_1: the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3. θ_2: the angle with the normal of the solvent plane, defined by the same three atoms, or, when the option -v23 is set, the angle with the vector between atoms 2 and 3. 2

Re: [gmx-users] Regarding finding orientation of angles of solvent with desired atom

2017-04-24 Thread Dilip H N
tps://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22> <#> On Mon, Apr 24, 2017 at 1:22 PM, Dilip H N <cy16f01.di...@nitk.edu.in> wrote: > Hello, > > I have simulated amino acid (eg., glycine) with w

[gmx-users] Regarding calculation of angles

2017-04-09 Thread Dilip H N
Hello, I have ran a amino acid simulation, and i want to calculate the angle between the atoms in amino acid molecule. how can i calculate it..?? gmx angle [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-od [<.xvg>]].. 1] here what index does it refer to .?? is it similar to th

[gmx-users] Regarding finding orientation of angles of solvent with desired atom

2017-04-24 Thread Dilip H N
Hello, I have simulated amino acid (eg., glycine) with water solvent mixture in gromacs.. my question is .. 1] How can i find out the solvent orientation (angle made) ie.,angle made by water (HOH) with respect to alpha carbon of amino acid (eg., glycine)...?? 2] I have tried with gmx sorient

[gmx-users] Regarding calculating the water orientation profile

2017-11-22 Thread Dilip H N
Hello Sir, I have run a simulation of amino-acid (glycine) with water molecules for 10 ns. Now i need to find out/analyze that whether the water molecules are getting/more oriented towards N-terminal of glycine or towards the C-terminal of glycine. (i hope this is what water orientation profile

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

2018-09-12 Thread João Henriques
. N. about this subject (on and off the mailing list). A simple query fetched 26 results: https://www.mail-archive.com/search?l=gromacs.org_gmx-users%40maillist.sys.kth.se=dilip+h+n+angle=0=0 Play with the query a bit and it should get you a lot of info on your problem. Best regards, João

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

2018-09-12 Thread rose rahmani
ching the mailing list before posting > is > > > usually good practice. If then something remains unclear, please feel > > free > > > to ask. I remember having quite long discussions with a Dilip H. N. > about > > > this subject (on and off the mailing list

Re: [gmx-users] Regarding analysing cos theta distribution functions

2017-04-12 Thread Mark Abraham
Hi, I have no idea what a cos theta distribution is, nor the objective of your study, so it's hard to help. But gmx mk_angndx is intended to help with such cases. Mark On Wed, Apr 12, 2017 at 8:17 AM Dilip H N <cy16f01.di...@nitk.edu.in> wrote: > Hello Jonathan, > > Suppose i wa

Re: [gmx-users] Regarding analysing cos theta distribution functions

2017-04-12 Thread Dilip H N
ograms/gmx-make_ndx.html > > Best of luck, > Jonathan > > On Tue, Apr 11, 2017 at 10:26 PM, Dilip H N <cy16f01.di...@nitk.edu.in> > wrote: > > > gmx sorient -f .xtc/trr -s .tpr -n .ndx... > > > > How to make these indexes for this case..?? what are the atoms

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

2018-09-12 Thread rose rahmani
remains unclear, please feel free > to ask. I remember having quite long discussions with a Dilip H. N. about > this subject (on and off the mailing list). > > A simple query fetched 26 results: > > https://www.mail-archive.com/search?l=gromacs.org_gmx-users%40maillist.sys.kth.se=dilip

Re: [gmx-users] Regarding calculating the water orientation profile

2017-11-24 Thread João Henriques
this in detail when I suggested looking at the angular probability function, defining the vectors you want to compute the angle from, etc. I really don't understand what is hindering you from performing such analysis, which seems to be exactly what you want/need. J On Fri, Nov 24, 2017 at 9:08 AM, Dilip H

Re: [gmx-users] Regarding calculating the water orientation profile

2017-11-23 Thread Mark Abraham
? Mark On Thu, 23 Nov 2017 07:26 Dilip H N <cy16f01.di...@nitk.edu.in> wrote: > Hello Sir, > I have run a simulation of amino-acid (glycine) with water molecules for 10 > ns. Now i need to find out/analyze that whether the water molecules are > getting/more oriented towards N-t

Re: [gmx-users] Regarding analysing cos theta distribution functions

2017-04-12 Thread Dilip H N
Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > There's lots of options... see > http://manual.gromacs.org/documentation/2016.3/user- > guide/cmdline.html#commands-by-topic > for > starters. > > Mark > > On Wed, Apr 12, 2017 at 10:06 AM Dilip H N <cy

Re: [gmx-users] Regarding calculating the water orientation profile

2017-11-23 Thread Mark Abraham
Hi, "Coming closer" implies you care about distance, but your original question was about orientation. So it's unclear what you want. Mark On Thu, 23 Nov 2017 16:50 Dilip H N <cy16f01.di...@nitk.edu.in> wrote: > I want to calculate whether the water molecules are coming clo

Re: [gmx-users] Regarding calculating the water orientation profile

2017-11-23 Thread Dilip H N
ke to need to be more clear about what you want to calculate > before you can sensibly find a tool to do it. You should be able to write > down the equation for what you want to compute as your observation long > before you run a simulation, or how will you know what data to collect? > >

Re: [gmx-users] Regarding calculating the water orientation profile

2017-11-23 Thread João Henriques
, Dilip H N <cy16f01.di...@nitk.edu.in> wrote: > I want to calculate whether the water molecules are coming closer towards > the N-terminal or towards the C-terminal of the amino-acid throughout the > simualtion. > And hence it can shed some light on the Hydrogen bond >

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 154, Issue 67

2017-02-16 Thread João Henriques
ect line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. gmx gangle (Jo?o Henriques) > 2. Re: gmx gangle (Antonio Baptista) >3. Re: Regarding topology... (Dilip H N) >4. Doubt from topolo

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

2018-09-12 Thread Nick Johans
> > > Thank you Joao, > > > > > > > > On Wed, 12 Sep 2018, 14:04 João Henriques, < > > joao.m.a.henriq...@gmail.com > > > > > > > > wrote: > > > > > > > > > Dear Rose, > > > > > > &

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

2018-09-12 Thread Nick Johans
>> > > I hope this is at least somewhat useful. >> > > >> > > Cheers, >> > > João >> > > >> > > >> > > >> > > On Wed, Sep 12, 2018 at 3:41 PM rose rahmani >> > > wrote: >> > > >

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

2018-09-12 Thread João Henriques
> > wrote: > > > > > > > Dear Rose, > > > > > > > > Spamming is not the answer. There have been quite a few threads about > > > this > > > > subject in the recent past. Searching the mailing list before posting > > is >

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

2018-09-12 Thread João Henriques
:41 PM rose rahmani >> > wrote: >> > >> > > Thank you Joao, >> > > >> > > On Wed, 12 Sep 2018, 14:04 João Henriques, < >> joao.m.a.henriq...@gmail.com >> > > >> > > wrote: >> > > >> > >

Re: [gmx-users] Regarding analysing cos theta distribution functions

2017-04-12 Thread João Henriques
ta distribution is, nor the objective of your > study, so it's hard to help. But gmx mk_angndx is intended to help with > such cases. > > Mark > > On Wed, Apr 12, 2017 at 8:17 AM Dilip H N <cy16f01.di...@nitk.edu.in> > wrote: > > > Hello Jonathan, > > &

Re: [gmx-users] Regarding calculating the water orientation profile

2017-11-23 Thread Dilip H N
ugh > > the mailing list, because I'm pretty sure this type of analysis has been > > discussed here more than once. > > > > Cheers, > > J > > > > On Thu, Nov 23, 2017 at 4:41 PM, Dilip H N <cy16f01.di...@nitk.edu.in> > > wrote: > > > >

Re: [gmx-users] Regarding calculating the water orientation profile

2017-11-24 Thread Mark Abraham
Hi, Why do you want to do something when you don't understand what it is or whether it will be useful? Mark On Fri, Nov 24, 2017 at 9:08 AM Dilip H N <cy16f01.di...@nitk.edu.in> wrote: > So what exactly does this Orientation Profile means.?? > I am really confused with the ex

Re: [gmx-users] Regarding calculating the water orientation profile

2017-11-24 Thread Dilip H N
il_medium=signature_campaign=signaturevirality> On Fri, Nov 24, 2017 at 12:47 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > "Coming closer" implies you care about distance, but your original question > was about orientation. So it's unclear what you want. > >

Re: [gmx-users] Regarding calculation of Hydrogen-Bond

2018-03-15 Thread Joe Jordan
. using MDAnalysis where it is pretty easy to redefine the h-bond donors and acceptors. On Thu, Mar 15, 2018 at 4:57 AM, Dilip H N <cy16f01.di...@nitk.edu.in> wrote: > 1) I tried with the Nitrogen atom of glycine and the oxygen atom of water > also using the command > > gmx hbo

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

2018-09-12 Thread João Henriques
> A simple query fetched 26 results: > > > > > https://www.mail-archive.com/search?l=gromacs.org_gmx-users%40maillist.sys.kth.se=dilip+h+n+angle=0=0 > > I search and read about but it didn't help me. It gives me the histogram of > angles but what i really want is the dis

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

2018-09-12 Thread João Henriques
> > Best > >> > > >> > > > >> > > I hope this is at least somewhat useful. > >> > > > >> > > Cheers, > >> > > João > >> > > > >> > > > >> > > > >> >

Re: [gmx-users] Regarding analysing cos theta distribution functions

2017-04-12 Thread Dilip H N
; > > On Wed, Apr 12, 2017 at 8:19 AM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > > > Hi, > > > > I have no idea what a cos theta distribution is, nor the objective of > your > > study, so it's hard to help. But gmx mk_angndx is intended to help with &

Re: [gmx-users] Regarding analysing cos theta distribution functions

2017-04-12 Thread Mark Abraham
Hi, There's lots of options... see http://manual.gromacs.org/documentation/2016.3/user-guide/cmdline.html#commands-by-topic for starters. Mark On Wed, Apr 12, 2017 at 10:06 AM Dilip H N <cy16f01.di...@nitk.edu.in> wrote: > Thank you Mark, João Henriques. > I have ran a Md simulat

Re: [gmx-users] Regarding analysing cos theta distribution functions

2017-04-12 Thread Mark Abraham
a distribution is, nor the objective of > your > > study, so it's hard to help. But gmx mk_angndx is intended to help with > > such cases. > > > > Mark > > > > On Wed, Apr 12, 2017 at 8:17 AM Dilip H N <cy16f01.di...@nitk.edu.in> > > wrote: > >

Re: [gmx-users] Regarding calculating the water orientation profile

2017-11-23 Thread João Henriques
ng to something similar sometime ago, and I'm > almost sure the post was yours. It may be a good idea to rummage through > the mailing list, because I'm pretty sure this type of analysis has been > discussed here more than once. > > Cheers, > J > > On Thu, Nov 23, 2017 at 4:41 P

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

2018-09-12 Thread João Henriques
omething > > > >> > > like this <https://pubs.acs.org/doi/abs/10.1021/jp0604241> (see > > > >> Figures > > > >> > 3 > > > >> > > and 5). Well, I've played around with a similar problem and > > there's > > > no > > > >> > >

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

2018-09-12 Thread rose rahmani
> > >> > > > >> > > > https://www.mdanalysis.org/docs/documentation_pages/analysis/waterdynamics.html > > >> > > > > > >> > > (click on the link, see 4.8.3.1.3. AngularDistribution). > > >> > > > >>

Re: [gmx-users] Restraining Protein-ligand distance

2017-03-31 Thread Juan José Galano Frutos
ackerell.umaryland.edu/~jalemkul > > == > > > -- > > Message: 4 > Date: Mon, 27 Mar 2017 12:57:36 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: