Re: [gmx-users] g_sdf -> and g_spatial

Dallas Warren wrote: I know, bit of a zombie topic (May 2011) to be digging out of the archives here. I have previously used g_sdf rather extensively and needed to generate some spatial distribution functions for a paper. Started to looked into g_spatial to see if that can do what I want it t

[gmx-users] g_sdf -> and g_spatial

I know, bit of a zombie topic (May 2011) to be digging out of the archives here. I have previously used g_sdf rather extensively and needed to generate some spatial distribution functions for a paper. Started to looked into g_spatial to see if that can do what I want it to, since g_sdf has been

Re: [gmx-users] g_sdf

Nilesh Dhumal wrote: Hello, I have a system with glucose + ionic liquids (cation + anion). I am trying calculate distribution of cation and anion around glucose molecule using g_sdf. I want to plot distribution of cation and anion is same figure. I run the following command g_sdf -f 3.trr -s

[gmx-users] g_sdf

Hello, I have a system with glucose + ionic liquids (cation + anion). I am trying calculate distribution of cation and anion around glucose molecule using g_sdf. I want to plot distribution of cation and anion is same figure. I run the following command g_sdf -f 3.trr -s 3.tpr -n glu-emi-dmp-128

Re: [gmx-users] g_sdf

Nilesh Dhumal wrote: Hello, I am trying to calculate g_sdf for my system (ionic liquids + water). I interested in distribution of anions and waters around cations. I used following command g_sdf -f 3.trr -n emi-etso4-64-no.ndx -s 3.tpr -o -r -mode 2 I found all the corrdinates in refmol.gro

[gmx-users] g_sdf

Hello, I am trying to calculate g_sdf for my system (ionic liquids + water). I interested in distribution of anions and waters around cations. I used following command g_sdf -f 3.trr -n emi-etso4-64-no.ndx -s 3.tpr -o -r -mode 2 I found all the corrdinates in refmol.gro are zero. I calculated

[gmx-users] g_sdf

Hello, I am trying to calculate g_sdf for my system (ionic liquids + water). I interested in distribution of anions and waters around cations. I used following command g_sdf -f 3.trr -n emi-etso4-64-no.ndx -s 3.tpr -o -r -mode 2 I found all the corrdinates in refmol.gro are zero. I calculated

RE: [gmx-users] g_sdf : error

omacs.org [mailto:gmx-users- >> boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18 May >> 2010 11:21 AM >> To: Discussion list for GROMACS users >> Subject: RE: [gmx-users] g_sdf : error >> >> >> Here are details. >> the first

RE: [gmx-users] g_sdf : error

nal Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of Nilesh Dhumal > Sent: Tuesday, 18 May 2010 11:21 AM > To: Discussion list for GROMACS users > Subject: RE: [gmx-users] g_sdf : error > > Here are details. > the

RE: [gmx-users] g_sdf : error

9903 9167 > - > When the only tool you own is a hammer, every problem begins to resemble > a nail. > > >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: T

RE: [gmx-users] g_sdf : error

> boun...@gromacs.org] On Behalf Of Nilesh Dhumal > Sent: Tuesday, 18 May 2010 9:29 AM > To: Discussion list for GROMACS users > Subject: RE: [gmx-users] g_sdf : error > > hey > Sorry for typing mistake. > I used ths command. > g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.t

RE: [gmx-users] g_sdf : error

>> From: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18 May >> 2010 5:55 AM >> To: gmx-users@gromacs.org >> Subject: [gmx-users] g_sdf : error >> >> >> Hello, >> I am try

RE: [gmx-users] g_sdf : error

iginal Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of Nilesh Dhumal > Sent: Tuesday, 18 May 2010 5:55 AM > To: gmx-users@gromacs.org > Subject: [gmx-users] g_sdf : error > > Hello, > I am trying to run g_sdf for

[gmx-users] g_sdf : error

Hello, I am trying to run g_sdf for sovlation for glucose in ionic liquids. I am trying to find distribution of anion around glucose. g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r First three group I selected from the same residue (Glucose). Forth grouup I selected from

Re: [gmx-users] g_sdf

Hello Justin, Sorry. I was following the manual-4.0 for g_spatial. Maunal is giving differnet things. I checked with g_spartial -h. I got. Thanks NIlesh On Tue, May 11, 2010 4:22 pm, Justin A. Lemkul wrote: > > > > Nilesh Dhumal wrote: > >> Hello Justin, >> I am doing solvation of glucose in ion

Re: [gmx-users] g_sdf

Nilesh Dhumal wrote: Hello Justin, I am doing solvation of glucose in ionic liquids. I want to show that glucose in surrounded by cation by ploting the iso-surface. Becuase of this I am using g_sdf. THe out put file is in .plt file. Can I get use gassview to plot the iso-surface. I have no i

Re: [gmx-users] g_sdf

Hello Justin, I am doing solvation of glucose in ionic liquids. I want to show that glucose in surrounded by cation by ploting the iso-surface. Becuase of this I am using g_sdf. THe out put file is in .plt file. Can I get use gassview to plot the iso-surface. Do you think still I can use g_spatial

Re: [gmx-users] g_sdf

Nilesh Dhumal wrote: Hello, I am trying to calculate spatial distribution function (SDF) for my system. Can I genrate the *.cube file or gaussian format file using sdf? I want to use gassview or molden software to plot. Have you tried g_spatial -h? I think you will find what you're looking

[gmx-users] g_sdf

Hello, I am trying to calculate spatial distribution function (SDF) for my system. Can I genrate the *.cube file or gaussian format file using sdf? I want to use gassview or molden software to plot. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

RE: [gmx-users] g_sdf and visualizing using gOpenMol

FYI, there is a listing in bugzilla http://bugzilla.gromacs.org/show_bug.cgi?id=356 Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation <>-- gmx-users mailing listgmx-users@gromacs

RE: [gmx-users] g_sdf and visualizing using gOpenMol

t has undergone a polar transformation -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Dallas B. Warren Sent: Wed 12/16/2009 8:25 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] g_sdf and visualizing using gOpenMol Rename it to .plt might be a good

RE: [gmx-users] g_sdf and visualizing using gOpenMol

: Tue 12/15/2009 11:41 PM To: gmx-users@gromacs.org Subject: [gmx-users] g_sdf and visualizing using gOpenMol Hi, I have a mesoporous silica with attached organic surface groups (alkyl chains). I am trying to quantify to what extent these surface groups interact with the mesoporous silica

[gmx-users] g_sdf and visualizing using gOpenMol

Hi, I have a mesoporous silica with attached organic surface groups (alkyl chains). I am trying to quantify to what extent these surface groups interact with the mesoporous silica surface they are attached to (as opposed to projecting straight into the pore space). I thought about using t

Re: [gmx-users] g_sdf gives wrong refmol with multiple center molecules

Hi, just for reference, I have filed a bug report on this (and one other issue with g_sdf): http://bugzilla.gromacs.org/show_bug.cgi?id=356 Best, Ondrej On Tue, Nov 10, 2009 at 16:35, Rasmus "Termo" Lundsgaard wrote: > Hi Atte > > Did you find a solution to this problem?? I'm doing the same c

[gmx-users] g_sdf gives wrong refmol with multiple center molecules

Hi Atte Did you find a solution to this problem?? I'm doing the same calculations as you describe, and wanted to try it out on TIP4p water first - which gives the wrong coordinates for the ref molecule by the -r flag as you described?!? The distribution looks completely right though... Anyo

RE: [gmx-users] g_sdf

That is entirely up to you. The forth paragraph in the help explains how the three atoms in the index are used to generate the coordinate system. Best idea with anything like this, have a play, see what comes out, see if it is what you want, then try again. Play with it like that will also help

[gmx-users] g_sdf

Dear Dr.Warren Thanks for your help about g_sdf. Actually I am confused about determine of the atoms (three reference atoms for the molecule) in index. I don't know on a basis of which criteria should I choose this three atoms inside the protein? Before thanks ___

RE: [gmx-users] g_sdf

What exactly your issue with using g_sdf? You need to supple a trajectory, index, and topology. Index contains the three reference atoms for the molecule, plus the atom you are calculating the sdf to. Selection of the correct grid size and binwidth is required to get something that looks as you

[gmx-users] g_sdf

Dear gmax user I want to use G_SDF command. But the description of this comand is alittle bit complicate for me. I want to compute the density of water around protein and I dont know could I do it or not. I will be thankful if somebody suggest me by this command. Thanks _

[gmx-users] g_sdf gives wrong refmol with multiple center molecules

Hi, if you give g_sdf just one molecule (in mode 1) to look at the distribution of other atoms around it, everything looks fine. However, if you give two or more molecules, the refmol.gro that is printed is messed up, but the actual density map still looks ok. You can try this with the 216 wa

[gmx-users] g_sdf reference configuration question

I'm getting odd behavior with the reference configuration generated by g_sdf (v. 3.3.3). I am wondering if this is a bug, and if the spatial density profile is similarly affected. My test system has simple, regular geometry: a glycine 15-mer held frozen in a fully extended "rod-like" configuratio

[gmx-users] G_SDF if reference atoms are in different residues

You could use g_spatial instead as that program requires you to do the reference calculation yourself with trjconv. I have not tried g_sdf in a while, but if you still would rather use that program, then you might be able to trjconv your own alignment and then somehow fool g_sdf into not do

[gmx-users] G_SDF if reference atoms are in different residues

Dear Users, I want to calculate the spatial distribution function of lipid headgroups around a protein residue. Because I am using a coarse-grained model each 'residue' is a single CG particle. This means that when defining the 3 reference groups that define the local coordinate axes I have no

RE: [gmx-users] g_sdf again

:[EMAIL PROTECTED] On Behalf Of Qiao Baofu Sent: 30 March 2007 08:19 To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_sdf again 2007/3/29, Dallas B. Warren <[EMAIL PROTECTED]>: Syma, > I am using g_sdf to calculating the spatial distribution of > lipid headgroups

Re: [gmx-users] g_sdf again

2007/3/29, Dallas B. Warren <[EMAIL PROTECTED]>: Syma, > I am using g_sdf to calculating the spatial distribution of > lipid headgroups around other species in my system. > > The thing is when I get the gro file (produced by using the -r flag in > g_sdf) and then look at this in vmd or chimera

RE: [gmx-users] g_sdf again

Syma, > I am using g_sdf to calculating the spatial distribution of > lipid headgroups around other species in my system. > > The thing is when I get the gro file (produced by using the -r flag in > g_sdf) and then look at this in vmd or chimera with my > spatial density file (plt), the referen

[gmx-users] g_sdf again

Hi, I am using g_sdf to calculating the spatial distribution of lipid headgroups around other species in my system. The thing is when I get the gro file (produced by using the -r flag in g_sdf) and then look at this in vmd or chimera with my spatial density file (plt), the reference gro file is n

[gmx-users] g_sdf function in a 2D map

Hi to All! I am using the g_sdf and g_rdf functions to analyse the solvation of some molecules. With g_sdf I get nice 3D maps that describe the g_rdf ... however I would like to know how is it possible to produce 2D maps from these files (with contour lines for example). I am using Chimera t

Re: [gmx-users] g_sdf now uploaded to website

Florian Haberl wrote: Hi, On Friday 13 October 2006 09:04, Dallas B. Warren wrote: FYI, g_sdf is now available on the website for download. It generates a spatial distribution function of atom(s) around a reference molecule. It is a radial distribution function in three dimensions, rather tha

Re: [gmx-users] g_sdf now uploaded to website

Hi, On Friday 13 October 2006 09:04, Dallas B. Warren wrote: > FYI, g_sdf is now available on the website for download. > > It generates a spatial distribution function of atom(s) around a > reference molecule. It is a radial distribution function in three > dimensions, rather than one. > > http:

[gmx-users] g_sdf now uploaded to website

FYI, g_sdf is now available on the website for download. It generates a spatial distribution function of atom(s) around a reference molecule. It is a radial distribution function in three dimensions, rather than one. http://www.gromacs.org/contributed_by_users/task,doc_details/gid,72/ This scri

[gmx-users] g_sdf

Dear Gromacs-users, I would like to use the analysis tool g_sdf, but couldn't find in the download section. If someone has the file, would you like to send me that ? Does it work with gromacs-3.3.1? Thank you very much for your help in advance. best, Hwankyu. _

[gmx-users] g_sdf for Gromacs 3.3 or any other tool for Spatial Distributions .

Dear all, Does anybody have the g_sdf ported for GROMACS 3.3 ? The g_sdf is a program for calculations of Spatial Distribution Functions (SDFs). It is not from the official distribution - it is written by Christoph Freudenberger whom I am not able to find (his old e-mail is expired). I've got