Re: [gmx-users] RDF of water

On 7/31/13 12:18 PM, George Patargias wrote: Hi Justin Yes, it does look like Fig. 8.3 in the manual if I choose the OW atoms as the the two groups! So there must be a problem with the choice water-water or SOL-SOL for RDF groups. Indeed there would, because then (with -rdf atom) you're ca

Re: [gmx-users] RDF of water

Hi Justin Yes, it does look like Fig. 8.3 in the manual if I choose the OW atoms as the the two groups! So there must be a problem with the choice water-water or SOL-SOL for RDF groups. Many thanks! > > > On 7/31/13 10:49 AM, George Patargias wrote: >> Hello >> >> I am trying to calculate the

Re: [gmx-users] RDF of water

On 7/31/13 10:49 AM, George Patargias wrote: Hello I am trying to calculate the RDF of water with water for a 10 ns MD of pure SPC water simulation (3x3x3 nm box). I run g_rdf with the default -rdf option (atom). The problem is that the integration of the RDF curve up to the first minimum yie

Re: [gmx-users] rdf

On 7/13/13 1:13 PM, Ishwor wrote: Dear all,, I have calculated the radial distribution function .I have difficulties in clear understanding of the radial distribution function. I will be pleased if you provide me the link where i can get clear understanding of rdf Refer to manual sect

Re: [gmx-users] RDF output has no data

Sir I was using an old version. Now I used 4.5.5, it still gives me the same blank output file. Kindly suggest how to go about solving this Thanks On Sat, Apr 6, 2013 at 2:26 PM, Mark Abraham wrote: > On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy wrote: > > > There was no fatal error precedin

Re: [gmx-users] RDF output has no data

On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy wrote: > There was no fatal error preceding the output. After selecting the groups > following are the output on the screen > Reading frame 1 time0.100 > Warning: can not make broken molecules whole without a run input file, > don't

Re: [gmx-users] RDF output has no data

There was no fatal error preceding the output. After selecting the groups following are the output on the screen Reading frame 1 time0.100 Warning: can not make broken molecules whole without a run input file, don't worry, mdrun doesn't write broken molecules Reading frame20

Re: [gmx-users] RDF output has no data

On Fri, Apr 5, 2013 at 2:30 PM, Venkat Reddy wrote: > Dear users > > I have used AMBER MD package to run simulation for a solvent box. I am now > using the gromacs utility to calculate rdf as follows: > > g_rdf -f file.trr -s file.pdb -n rdf.ndx -o rdf.xvg > > However, I get no data in the output

Re: [gmx-users] RDF(PMF) and Umbrella sampling

have now negative distances in pullx.xvg. I don't know if the fact that we now have negative numbers makes any problem for WHAM (from the *.tpr we would expect that we have only positive numbers). Wish you luck. greetings thomas Date: Tue, 10 Jan 2012 10:47:43 +0000 From: Gavin Mela

Re: [gmx-users] RDF(PMF) and Umbrella sampling

ian, you > couldn't say anything. > > > >> Date: Tue, 10 Jan 2012 10:47:43 +0000 >> From: Gavin Melaugh >> Subject: Re: [gmx-users] RDF(PMF) and Umbrella sampling >> To: Discussion list for GROMACS users >> Message-ID:<4f0c174f.2050...@qub.ac.uk>

Re: [gmx-users] RDF(PMF) and Umbrella sampling

distances. For this case it would be easy to correct the histogram. But if the histogram isn't a perfect gaussian, you couldn't say anything. Date: Tue, 10 Jan 2012 10:47:43 + From: Gavin Melaugh Subject: Re: [gmx-users] RDF(PMF) and Umbrella sampling To: Discussion list for GRO

Re: [gmx-users] RDF(PMF) and Umbrella sampling

Hi Justin Again, many thanks for the reply. So when the COM distance changes sign, what effect does that have on the distribution of the COM distance about the mean value for that window i.e. If say my ref dist in 0 nm and the umbrella sampling allows the distance to sample distances say at 0.02 n

Re: [gmx-users] RDF(PMF) and Umbrella sampling

Gavin Melaugh wrote: Hi Justin Thanks very much. One last question. What do you mean when you say "COM reference distance is changing signs"? I thought the COM distance was the absolute distance between the two groups and therefore cannot be negative? The pull code deals in vectors. Signs

Re: [gmx-users] RDF(PMF) and Umbrella sampling

Hi Justin Thanks very much. One last question. What do you mean when you say "COM reference distance is changing signs"? I thought the COM distance was the absolute distance between the two groups and therefore cannot be negative? Cheers Gavin Dariush Mohammadyani wrote: > Hi Gavin, > > A ques

Re: [gmx-users] RDF(PMF) and Umbrella sampling

Gavin Melaugh wrote: Hi Justin Just a quick clarification regarding my previous point. With geometry = distance, and pull_dim =Y Y Y . Is the pull_group sampling all dimensions equally (or without prejudice) about pull_init ? And iN your I don't necessarily know if you can say "equally," bu

Re: [gmx-users] RDF(PMF) and Umbrella sampling

Dariush Mohammadyani wrote: Hi Gavin, A question arose for me: why did you consider the (rate = 0)? During umbrella sampling one restrains the configuration; you don't steer it along the vector between the COM's of the two species. -Justin -- Ju

Re: [gmx-users] RDF(PMF) and Umbrella sampling

Hi Gavin, A question arose for me: why did you consider the (rate = 0)? Dariush On Fri, Jan 6, 2012 at 11:47 AM, Gavin Melaugh wrote: > Hi Justin > > Just a quick clarification regarding my previous point. With geometry = > distance, and pull_dim =Y Y Y . Is the pull_group sampling all > dime

Re: [gmx-users] RDF(PMF) and Umbrella sampling

Hi Justin Just a quick clarification regarding my previous point. With geometry = distance, and pull_dim =Y Y Y . Is the pull_group sampling all dimensions equally (or without prejudice) about pull_init ? And iN your first reply what did you mean about by "straight pull" ? Cheers Gavin Justin

Re: [gmx-users] RDF(PMF) and Umbrella sampling

O.K cheers Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi Justin >> >> Thanks for the reply. I wanted my "pulling" to be free in all >> directions, that is in the liquid state with no defined reaction >> coordinate i.e not along a specific axis. This is why I used geometry = >> distance.

Re: [gmx-users] RDF(PMF) and Umbrella sampling

Gavin Melaugh wrote: Hi Justin Thanks for the reply. I wanted my "pulling" to be free in all directions, that is in the liquid state with no defined reaction coordinate i.e not along a specific axis. This is why I used geometry = distance. Would you agree with this approach? I suppose there

Re: [gmx-users] RDF(PMF) and Umbrella sampling

Hi Justin Thanks for the reply. I wanted my "pulling" to be free in all directions, that is in the liquid state with no defined reaction coordinate i.e not along a specific axis. This is why I used geometry = distance. Would you agree with this approach? By free I mean. The absolute distance betwe

Re: [gmx-users] RDF(PMF) and Umbrella sampling

Gavin Melaugh wrote: Dear all I have a query regarding umbrella sampling simulations that I have carried out to study a dynamical process of a guest inserting into a host. I always get get a wall tending off to infinity at or just before the zero distance between the two species. The process I

Re: [gmx-users] RDF - first minimum of O-O

On Sun, Sep 18, 2011 at 7:25 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > > >> >> On Sun, Sep 18, 2011 at 5:52 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Steven Neumann wrote: >> >> >> >>On Sun, Sep 18, 2011 at 5:07 PM, Mark Abraham >>>

Re: [gmx-users] RDF - first minimum of O-O

Steven Neumann wrote: On Sun, Sep 18, 2011 at 5:52 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: On Sun, Sep 18, 2011 at 5:07 PM, Mark Abraham mailto:mark.abra...@anu.edu.au>

Re: [gmx-users] RDF - first minimum of O-O

On Sun, Sep 18, 2011 at 5:52 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > > >> >> On Sun, Sep 18, 2011 at 5:07 PM, Mark Abraham >> > mark.abra...@anu.edu.**au >> wrote: >> >>On 19/09/2011 2:02 AM, Steven Neumann wrote: >> >>Hi Gromacs Users, >>Can anyone explain

Re: [gmx-users] RDF - first minimum of O-O

Steven Neumann wrote: On Sun, Sep 18, 2011 at 5:07 PM, Mark Abraham > wrote: On 19/09/2011 2:02 AM, Steven Neumann wrote: Hi Gromacs Users, Can anyone explain me why in g_bond the distance is takes <= 3.5nm. If you mean g_hbond, and

Re: [gmx-users] RDF - first minimum of O-O

On Sun, Sep 18, 2011 at 5:07 PM, Mark Abraham wrote: > On 19/09/2011 2:02 AM, Steven Neumann wrote: > >> Hi Gromacs Users, >> Can anyone explain me why in g_bond the distance is takes <= 3.5nm. >> > > If you mean g_hbond, and are using units incorrectly, 0.35nm would be a > characteristic distance

Re: [gmx-users] RDF - first minimum of O-O

On 19/09/2011 2:02 AM, Steven Neumann wrote: Hi Gromacs Users, Can anyone explain me why in g_bond the distance is takes <= 3.5nm. If you mean g_hbond, and are using units incorrectly, 0.35nm would be a characteristic distance cut-off for deciding whether a hydrogen bond might exist It

Re: [gmx-users] rdf

On 14/06/2011 10:11 PM, Nilesh Dhumal wrote: Hello, I have a system with 128 emi (cations) and 128 Cl (anions). I want to study is there any bifurcated interaction between hydrogen of cation and CL atoms or CL atom interacting with 2 different hydrogen of cation. For this I considered all CL a

Re: [gmx-users] rdf wrong convergence

On 17/11/2010 8:07 PM, Raymond wrote: I built a system with 2 bulks .left side is liquid side right is gas . But the convergence of the rdf only liquid I calculated is more than 1(about 1.3) . I make a comparison with the Previously work I did (liquid only without gas ) the trend is totally sa

RE: [gmx-users] RDF converge to zero than 1, why?

nal Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of tekle...@ualberta.ca > Sent: Thursday, 16 September 2010 4:34 AM > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] RDF converge to zero than 1, why? > > > Dear Ju

Re: [gmx-users] RDF converge to zero than 1, why?

On 2010-09-15 21.04, tekle...@ualberta.ca wrote: Thank you David, So this means my result is correct! and I have to add an explanation that my system is hetrogeneous only. There is nothing wrong then with my system. You can test the RDF normalization etc. by integrating 4 Pi r^2g(r)dr, that s

Re: [gmx-users] RDF converge to zero than 1, why?

Thank you David, So this means my result is correct! and I have to add an explanation that my system is hetrogeneous only. There is nothing wrong then with my system. Rob Quoting "David van der Spoel" : On 2010-09-15 20.34, tekle...@ualberta.ca wrote: Dear Justine, Then my guess is yo

Re: [gmx-users] RDF converge to zero than 1, why?

On 2010-09-15 20.34, tekle...@ualberta.ca wrote: Dear Justine, Then my guess is you don't have a PBC problem, but perhaps a convergence problem. You're only analyzing 1 ns of data; I don't know what implication that will have for your outcome. I have read about this problem and some people s

Re: [gmx-users] RDF converge to zero than 1, why?

Dear Justine, Then my guess is you don't have a PBC problem, but perhaps a convergence problem. You're only analyzing 1 ns of data; I don't know what implication that will have for your outcome. I have read about this problem and some people suggested that my box expanded a lot means I

Re: [gmx-users] RDF

To: Discussion list for GROMACS users Date: Sat, 14 Aug 2010 12:10:44 +0200 Subject: Re: [gmx-users] RDF On 2010-08-14 11.55, Jafar Azamat wrote: > Hi all Gromacs users > How can report RDF for the centers of the geometry of molecules? > > try g_rdf -h and read which options

Re: [gmx-users] RDF

On 2010-08-14 11.55, Jafar Azamat wrote: Hi all Gromacs users How can report RDF for the centers of the geometry of molecules? try g_rdf -h and read which options you have. com with respect to com of another group is not possible it seems. Jafar Azamat Molecular Simulations Lab. Faculty of

Re: [gmx-users] RDF

On 2010-08-03 19.37, Nisha Patel wrote: Hello, I would like to understand how gromacs does RDF normalization for the volume and the density. I am not sure if I understand it correctly, but is it just that rdf multiplied by (number of frames*volume of each shell)/ total volume ? Thanks. It

Re: [gmx-users] RDF

Hello, On 27.04.2010, at 23:31, Nilesh Dhumal wrote: > Hello, > I am trying to plot radial distribution function between a atom and a > center of two atoms. > How can I calculate the centre of two atoms and further how can I use this > center to plot radial distribution funciton? > you will ha

RE: [gmx-users] rdf problem

If you have aggregation and a small box size, then the rdf will not be able to asymptote to one. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.ed

RE: [gmx-users] rdf problem

> Date: Tue, 9 Mar 2010 10:39:01 +0100 > From: er...@xray.bmc.uu.se > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] rdf problem > > Antonia V. skrev: > > Dear all, > > > > I am simulating a binary system of two non mixing components (5CB and >

Re: [gmx-users] rdf problem

Antonia V. skrev: Dear all, I am simulating a binary system of two non mixing components (5CB and water using version 4-0-3; the whole equilibrated trajectory is about 300ns). I want to calculate the rdf of the centers of mass of 5CB using the command g_rdf -f traj300.xtc -rdf mol_com -o rdf

Re: [gmx-users] rdf

okay this should work http://docs.google.com/fileview?id=0B_QNmYARywUiNzE0MDA0NWMtYjFiMy00MTRjLThkNDMtNTk3NDgyNjcxZTgx&hl=en -Nisha Quoting chris.ne...@utoronto.ca: I didn't get the attachment. Please upload the image to some website and post the link. --original message -- I saved my r

RE: [gmx-users] rdf

problem begins to resemble a nail. > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of nishap.pa...@utoronto.ca > Sent: Monday, 1 February 2010 9:57 AM > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] rdf &

Re: [gmx-users] rdf

Hi, I saved my rdf plot as a pdf file and I have attached it to this email. Hopefully it will work. My system is one methane with 893 molecules of tip3p water in a cubic box of size 3 3 3 (nm). My topology file is : ; Include forcefield parameters #include "ffoplsaa.itp" [ moleculetyp

Re: [gmx-users] rdf

nishap.pa...@utoronto.ca wrote: Hi Will, I have been using pme from the very start and it didn't help with the volume. Could you please elaborate on what you mean by average g(r) over every molecule? And because my rdf-s are not smooth enough even with 100ns, I get fluctuating data

Re: [gmx-users] rdf

Hi Will, I have been using pme from the very start and it didn't help with the volume. Could you please elaborate on what you mean by average g(r) over every molecule? And because my rdf-s are not smooth enough even with 100ns, I get fluctuating data using rdf-s. -Nisha Quoti

Re: [gmx-users] rdf

Hi, 100 ns is overkill for those liquids. It should be smooth enough at 1 ns, provided you average g(r) over every molecule. What do you mean the volume decreases? With time? As for the cut-off, it's well known that switching Coulomb terms leads to artifacts, and increasing the cut-off distanc

Re: [gmx-users] RDF methanol and water

nishap.pa...@utoronto.ca wrote: HI, Okay, so I am trying to plot rdf of one methanol this time in water. Is there a way to select methanol molecule as a whole (i.e. get rdf from the center of the molecule), instead of Me, O and H. Even though I put Me, O and H in same group, I am getting a

Re: [gmx-users] RDF plot. This is weird!

Lum Nforbi wrote: Dear all, I have attached a RDF plot of 2000 molecules of water (SOL is the system name). It does not follow the normal trend. I used the command line below to get this plot: g_rdf -f wfullmdrun_traj.xtc -s wfullmdrun_extend3.tpr -o wfullmdrun_rdf.xvg The run took about 1

Re: [gmx-users] RDF in GMX 4

Eudes Fileti wrote: Hello, everyone, in earlier versions of the Gromacs the option to calculate rdf between center of mass (com-com) was not implemented. Is this option implemented in version 4.0? If no, someone would have suggestion to calculate the RDF com-com for liquid benzene? From g_r

Re: [gmx-users] RDF values lower than 1

Argyrios Karatrantos wrote: Hi, i calculate the RDF from NVT simulation of a solution of polyelectrolyte chains and their counterions. The RDF calculated is between the monomers of the chains and the counterions. I would expect that the equilibrated value of RDF would be 1. However it is alway

Re: [gmx-users] rdf bug in 3.3.1 depending on the gcc?

Hi, okay I will submit the bugzilla. Thanks Regards, andrea David van der Spoel wrote: > andrea spitaleri wrote: >> Hi all, >> I have suspicious that g_rdf is bugged or at least it has a problem >> depending on the machine type. >> In one pc works and in another it hangs in "Reading frame 0.

Re: [gmx-users] rdf bug in 3.3.1 depending on the gcc?

andrea spitaleri wrote: Hi all, I have suspicious that g_rdf is bugged or at least it has a problem depending on the machine type. In one pc works and in another it hangs in "Reading frame 0. 0.". I should also to say that in the "PC not working" it hangs depending on the kind of select

Re: [gmx-users] rdf / sdf around a specific point

Am Mittwoch, 13. Dezember 2006 10:00 schrieb Tsjerk Wassenaar: > I'd say it would be easiest to modify the code of g_rdf/g_sdf to allow > the determination to be done around a given point. I don't know > whether you have any programming experience. It shouldn't be very > difficult to do. Maybe, if

Re: [gmx-users] rdf / sdf around a specific point

Hi Martin, I'd say it would be easiest to modify the code of g_rdf/g_sdf to allow the determination to be done around a given point. I don't know whether you have any programming experience. It shouldn't be very difficult to do. Maybe, if I have some spare time, I could do it, but it won't have m

Re: [gmx-users] rdf

On Tue, 31 Oct 2006, Claus Valka wrote: >Title : radial distribution function, 31.10.06 > > Hello, > > I am a new user of Gromacs (just started my >Phd), and > I'm trying to calculate the partial radial >distibution functions > for a system of polymer chains. > >

RE: [gmx-users] rdf

Will be rather complex one to make I think. Part C is easy, use the make_ndx script to generate an index file with the following groups: all C CH3 H Then run g_rdf with each of the pairings you want. Personally don't know about the same chain / different chains th