[gmx-users] multi file input for index files

Dear users, I created two different index files (A.ndx and B.ndx). I want to run the two files at the same time. e.g. g_hbond -f traj.xtc -s run.tpr -num A-B.xvg -n A.ndx -n B.ndx where, I want to calculate the hydrogen bonds between A and B. This command is giving the error as it expected.

Re: [gmx-users] multi file input for index files

On 10/01/2012 7:13 PM, ahmet yıldırım wrote: Dear users, I created two different index files (A.ndx and B.ndx). I want to run the two files at the same time. e.g. g_hbond -f traj.xtc -s run.tpr -num A-B.xvg -n A.ndx -n B.ndx where, I want to calculate the hydrogen bonds between A and B. This

Re:[gmx-users]-Snapshots

Hi. You will need a visualization program like VMD to get a 3D representation of your system. After reading in the .gro file, you can edit representation details and take pictures. Greetings, Felix Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im

Re: [gmx-users] q question related to gromacsinstallation by cygwin

On 10/01/2012 5:45 PM, Dialing Pretty wrote: Dear Mark, If --disable-threads , how it will influence the function of GROMACS? By preventing you from running mdrun with a separate execution thread in parallel on each physical processor that your machine has. If you need parallel

Re: [gmx-users] dynamic libraries and static libraries

Hi As far as I know, static libraries are linked during compilation, thus are part of your installation, while shared libraries are linked during execution. The latter lead to, somehow, more robust binaries, as once they are compiled they have (almost) no dependences, while the latter save

Re: [gmx-users] multi file input for index files

Hi, But I want to calculate the hydrogen bonds between A and B groups. If I do as you said, I will have calculated intra hydrogen bonds of a group AB (merged A and B). 2012/1/10 Mark Abraham mark.abra...@anu.edu.au On 10/01/2012 7:13 PM, ahmet yıldırım wrote: Dear users, I created two

Re: [gmx-users] dynamic libraries and static libraries

On 10/01/2012 5:38 PM, Dialing Pretty wrote: Dear All, For GROMACS, what will be the difference by using static libraries and dynamic libraries? Static have fewer compatibility problems, but use rather more disk after installation. How can I install the static libraries and how can I

Re: [gmx-users] multi file input for index files

On 10/01/2012 7:45 PM, ahmet y?ld?r?m wrote: Hi, But I want to calculate the hydrogen bonds between A and B groups. If I do as you said, I will have calculated intra hydrogen bonds of a group AB (merged A and B). I didn't say to combine your groups. I said to put both group definitions in

RE: [gmx-users] multi file input for index files

So as you can see Gromacs does not support multi file input :) Create one index file and specify there your two groups. Then g_hbond will ask you to choose two groups from this file. Jan === Jan Marzinek PhD Candidate Centre for

Re: [gmx-users] multi file input for index files

Thanks Mark and Marzinek, The Problem is solved: g_hbond -f traj.xtc -s run.tpr -num AB.xvg -n AB.ndx chain A Found 1234 atoms with chain identifier A 19 chA : 1234 atoms name 19 chainA chain B Found 1234 atoms with chain identifier B 20 chB : 1234

Re: [gmx-users] Hello

Dear Gromacs users... I am new to gromacs... I have not understood this In your shell configuration file (e.g. .bashrc for bash or .cshrc/.tcshrcfor tcsh) you should use a command analogous to: source /usr/local/gromacs/bin/GMXRC near the end of that file. can any one please tell me what

Re: [gmx-users] Hello

On 10/01/2012 9:12 PM, Nirmal Prasad wrote: Dear Gromacs users... I am new to gromacs... I have not understood this In your shell configuration file (e.g. .bashrc for bash or .cshrc/.tcshrc for tcsh) you should use a command analogous to: source /usr/local/gromacs/bin/GMXRC near the end

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

[gmx-users] Energy Minimization

Dear Gmx Users, I am setting up my simulations of carbon tube with protein. I solvated my system, added ions and I would like to run EM of my system. My carbons of the tube in MD will be restrained. In this case should I run EM of my protein in water (and with ions) separately and the copy

Re: [gmx-users] Energy Minimization

On 10/01/2012 9:54 PM, Steven Neumann wrote: Dear Gmx Users, I am setting up my simulations of carbon tube with protein. I solvated my system, added ions and I would like to run EM of my system. My carbons of the tube in MD will be restrained. In this case should I run EM of my protein in

Re: [gmx-users] Energy Minimization

Thank you. Should I also copy and paste coordinates of my ions or just my protein? Steven On Tue, Jan 10, 2012 at 11:03 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/01/2012 9:54 PM, Steven Neumann wrote: Dear Gmx Users, I am setting up my simulations of carbon tube with protein. I

Re: [gmx-users] multi file input for index files

Hey, In cases where you do end up with two index files, like resulting from a script or so, you can also simply combine them by concatenation: cat A.ndx B.ndx C.ndx Of course you'll have to make sure that the group names are unique ;) Cheers, Tsjerk 2012/1/10 ahmet yıldırım

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

and then process with NVT and NPT or run EM with restrained nanotubes of my system directly? Thank you, Steven -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20120110/46237a45/attachment-0001.html

Re: [gmx-users] Energy Minimization

On 10/01/2012 10:13 PM, Steven Neumann wrote: Thank you. Should I also copy and paste coordinates of my ions or just my protein? The randomly-placed ions will be immaterial for EM. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] Hello

I got this message pdb2gmx: command not found but I installed gromacs..how to solve this error nirmal On Tue, Jan 10, 2012 at 3:48 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/01/2012 9:12 PM, Nirmal Prasad wrote: Dear Gromacs users... I am new to gromacs... I have not

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

/attachments/20120110/46237a45/attachment-0001.html -- inline: histo.png-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before

Re: [gmx-users] Energy Minimization

Thank you. Imagine I would like to put ligands in further simulations. Should I then copy coordinates of my ligands in smaller box (not to overlap my tube) and then copy both coordinates of ions and ligands plus protein? On Tue, Jan 10, 2012 at 11:31 AM, Mark Abraham mark.abra...@anu.edu.auwrote:

[gmx-users] homodimer simulation

Dear user, I simulated a homodimer of 238aa each with oplsaa forcefield using gromacs-4.5.3. But while calculating the rmsf plot I got a plot in which starting and ending residue were connected by a straight line along with the actual rmsf plot. Also the two rmsf plots that it gave were slightly

[gmx-users] Mixture of H2O and D2O

Dear gmx users I am trying to run a MD with a mixture of D2O and H2O. I defined a new itp spcdeut.itp for heavy water and the usualy spc.itp for normal water. when I try to run grompp appear this error: The [molecules] section of your topology specifies more than one block of a [moleculetype]

Re: [gmx-users] Hello

On 10/01/2012 10:37 PM, Nirmal Prasad wrote: I got this message pdb2gmx: command not found but I installed gromacs..how to solve this error You need a functional PATH. See http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation. Mark

Re: [gmx-users] Energy Minimization

On 10/01/2012 10:46 PM, Steven Neumann wrote: Thank you. Imagine I would like to put ligands in further simulations. Should I then copy coordinates of my ligands in smaller box (not to overlap my tube) and then copy both coordinates of ions and ligands plus protein? Any way you want to

Re: [gmx-users] Mixture of H2O and D2O

On 10/01/2012 10:35 PM, Hernan Ahumada wrote: Dear gmx users I am trying to run a MD with a mixture of D2O and H2O. I defined a new itp spcdeut.itp for heavy water and the usualy spc.itp for normal water. when I try to run grompp appear this error: The [molecules] section of your topology

[gmx-users] About g_msd. I want to plot the curve from 0.01ps.

Hi I have been learning how to use gromacs owing to your advice. I have simple question on g_msd. I tried to plot MSD curve using g_msd. I want to deeply investigate the MSD curve from 0.01ps to the last of simulation (my case, 1ns). However, g_msd always produce the MSD curve starting from

Re: [gmx-users] Hello

Dear Mark, Thank you very much..now its working nirmal On Tue, Jan 10, 2012 at 5:31 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/01/2012 10:37 PM, Nirmal Prasad wrote: I got this message pdb2gmx: command not found but I installed gromacs..how to solve this error You need a

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

The histograms are really crowded, it would be better to plot only the black one and probably the red one, to see the it better. Two ideas which can probably solve the problem (ok, both assume, that the host has a certain shape). You said you investigate guest-insertion to a host. I would

Re: [gmx-users] problem with gromacs

Hello, Thanks for the advice. For one moment everything was ok, but at some point appeared an error. $ cd gromacs-4.5.5 ./configure --disable-threads make .libs/xlate.o:xlate.c:(.text+0x774): undefined reference to `_save_free' .libs/xlate.o:xlate.c:(.text+0x7a0): undefined reference to

[gmx-users] how to model linear rigid molecules (CO2)

Hi, I need to model linear rigid molecules, CO2. I understood that the virtual site have to be introduced to model CO2 like below way. [ atomtypes ] ; type masschargeptype c6c12 D1 22.0049750. A 0. 0. D2

Re: [gmx-users] problem with gromacs

On 11/01/2012 12:32 AM, Sylwia Chmielewska wrote: Hello, Thanks for the advice. For one moment everything was ok, but at some point appeared an error. Use make distclean before configure if you have already configured and built and need to change stuff. Else things can get confused

Re: [gmx-users] About g_msd. I want to plot the curve from 0.01ps.

On 10/01/2012 11:21 PM, Kiwoong Kim wrote: Hi I have been learning how to use gromacs owing to your advice. I have simple question on g_msd. I tried to plot MSD curve using g_msd. I want to deeply investigate the MSD curve from 0.01ps to the last of simulation (my case, 1ns). However, g_msd

Re: [gmx-users] About g_msd. I want to plot the curve from 0.01ps.

Kiwoong Kim wrote: Hi I have been learning how to use gromacs owing to your advice. I have simple question on g_msd. I tried to plot MSD curve using g_msd. I want to deeply investigate the MSD curve from 0.01ps to the last of simulation (my case, 1ns). However, g_msd always produce the

[gmx-users] Regarding NVT NPT ensemble

Dear Sir, I am new user in Gromacs. I am using Gromacs for protein-ligand complex. If I am not wrong MD simulation have three part. 1. Energy Minimization 2. Equilibration phase 3. Production phase After EM minimization we run Equilibration using (NVT NPT ensemble). I have little sily

Re: [gmx-users] Regarding NVT NPT ensemble

On 11/01/2012 1:14 AM, ajani haresh wrote: Dear Sir, I am new user in Gromacs. I am using Gromacs for protein-ligand complex. If I am not wrong MD simulation have three part. 1. Energy Minimization 2. Equilibration phase 3. Production phase After EM minimization we run Equilibration using

[gmx-users] Re: gmx-users Digest, Vol 93, Issue 52

Thanks Sir, But I have one more question. If I run first NVT then NPT ensemble. So we get output file from NPT ensemble. NPT ensemble output we will use into production phase. Means they also take parameter from NVT ensemble. Thanks in advance Message: 6 Date: Wed, 11 Jan 2012 01:20:20

Re: [gmx-users] Regarding NVT NPT ensemble

ajani haresh wrote: Thanks Sir, But I have one more question. If I run first NVT then NPT ensemble. So we get output file from NPT ensemble. NPT ensemble output we will use into production phase. Means they also take parameter from NVT ensemble. The two ensembles work in concert to

Re: [gmx-users] homodimer simulation

Kavyashree M wrote: Dear user, I simulated a homodimer of 238aa each with oplsaa forcefield using gromacs-4.5.3. But while calculating the rmsf plot I got a plot in which starting and ending residue were connected by a straight line along with the actual rmsf plot. Also the two rmsf That's

[gmx-users] Coupling groups - Thermostat

Dear Gmx Users, My system includes: ions, water, two tubes made of carbon atoms, protein. I would like to run NVT (and then NPT) with position restarined dynamics of my protein and tubes. I am wondering whether this approach is good (two coupling groups: Protein_Tubes and Water_and_ions?? My

Re: [gmx-users] maxh not causing termination

On Mon, Jan 9, 2012 at 3:46 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 10/01/2012 7:19 AM, Ben Reynwar wrote: On Tue, Dec 20, 2011 at 7:16 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 12/19/2011 1:51 PM, Ben Reynwar wrote: I'm having a problem with gromacs not terminating as

[gmx-users] Concatenating RMSD plots

Hi there, I have just run several simulations of my system using different seeds and now i want to plot the RMSDs for different seeds in one plot for comparison. Is there any way to do it. Thanks Rohit -- Rohit Farmer PhD Biosciences (2011-2014) Center for Systems Biology University of

Re: Fw: [gmx-users] trjconv in martini

Hi Tsjerk, I know that my question is silly but please help me. I installed python2.5 on my system, then I ran ./xtcrev.py 1a.xtc 1a-rev.xtc but it gave me following error: Traceback (most recent call last):   File ./xtcrev.py, line 54, in module     n   = 92 + i(f.read(84)[-4:])   # Size

Re: [gmx-users] Coupling groups - Thermostat

Steven Neumann wrote: Dear Gmx Users, My system includes: ions, water, two tubes made of carbon atoms, protein. I would like to run NVT (and then NPT) with position restarined dynamics of my protein and tubes. I am wondering whether this approach is good (two coupling groups: Protein_Tubes

Re: [gmx-users] Concatenating RMSD plots

Rohit Farmer wrote: Hi there, I have just run several simulations of my system using different seeds and now i want to plot the RMSDs for different seeds in one plot for comparison. Is there any way to do it. Import multiple data sets into xmgrace. Alternatively, if they're all named

Re: [gmx-users] Coupling groups - Thermostat

On Tue, Jan 10, 2012 at 6:22 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, My system includes: ions, water, two tubes made of carbon atoms, protein. I would like to run NVT (and then NPT) with position restarined dynamics of my protein and tubes. I am

Re: [gmx-users] Coupling groups - Thermostat

On Tue, Jan 10, 2012 at 6:55 PM, Steven Neumann s.neuman...@gmail.comwrote: On Tue, Jan 10, 2012 at 6:22 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, My system includes: ions, water, two tubes made of carbon atoms, protein. I would like to run NVT

[gmx-users] Re: gmx-users Digest, Vol 93, Issue 54

On 10/01/12 18:56, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or

Re: [gmx-users] Concatenating RMSD plots

Rohit Farmer wrote: Hi there, I have just run several simulations of my system using different seeds and now i want to plot the RMSDs for different seeds in one plot for comparison. Is there any way to do it. Thanks Rohit Hi Justin, Thanks for the suggestion, I tried it and it works.

Re: [gmx-users] Coupling groups - Thermostat

Steven Neumann wrote: On Tue, Jan 10, 2012 at 6:55 PM, Steven Neumann s.neuman...@gmail.com mailto:s.neuman...@gmail.com wrote: On Tue, Jan 10, 2012 at 6:22 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx

Re: [gmx-users] Coupling groups - Thermostat

On Tue, Jan 10, 2012 at 7:07 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: On Tue, Jan 10, 2012 at 6:55 PM, Steven Neumann s.neuman...@gmail.commailto: s.neuman...@gmail.com** wrote: On Tue, Jan 10, 2012 at 6:22 PM, Justin A. Lemkul jalem...@vt.edu

Re: [gmx-users] Coupling groups - Thermostat

Steven Neumann wrote: On Tue, Jan 10, 2012 at 7:07 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: On Tue, Jan 10, 2012 at 6:55 PM, Steven Neumann s.neuman...@gmail.com mailto:s.neuman...@gmail.com

Re: [gmx-users] Cytochrom C

Does anybody know where can I find [ HIS ] parameters? Thanks, Dariush On Sat, Jan 7, 2012 at 3:58 AM, Dariush Mohammadyani d.mohammady...@gmail.com wrote: Dear Peter and Krzyszto, Thank you. I am following your comments. If I get any problem I will come back. On Fri, Jan 6, 2012 at

Re: [gmx-users] Cytochrom C

Dariush Mohammadyani wrote: Does anybody know where can I find [ HIS ] parameters? HIS is histidine; it's built into every one of the force fields in Gromacs. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee

Re: [gmx-users] Cytochrom C

Dear Justin, I could not find HIS in CHARMM and GROMOS53a6. Somebodies offer to rename it to HSE or HSD, but I do not know why? and which one is correct. I am working on Cytochorom c. Thanks, Dariush On Tue, Jan 10, 2012 at 4:22 PM, Justin A. Lemkul jalem...@vt.edu wrote: Dariush

Re: [gmx-users] Cytochrom C

Dariush Mohammadyani wrote: Dear Justin, I could not find HIS in CHARMM and GROMOS53a6. Somebodies offer to rename it to HSE or HSD, but I do not know why? and which one is correct. I am working on Cytochorom c. They refer to different protonation states, either epsilon or delta. The

Re: [gmx-users] Cytochrom C

Hi Dariush If you are using the CHARMM27 force field, then all topology and parameters are in your share/top/charmm27.ff directory The defined molecules are listed in aminoacids.rtp and force field parameters in numerous other files. CHARMM does not use 'HIS' for histidine, but has HSD, HSE

Re: [gmx-users] Coupling groups - Thermostat

On 11/01/2012 6:52 AM, Justin A. Lemkul wrote: Steven Neumann wrote: On Tue, Jan 10, 2012 at 7:07 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: On Tue, Jan 10, 2012 at 6:55 PM, Steven Neumann s.neuman...@gmail.com

[gmx-users] HEME topology

Hello, Can any one send topology for Heme group..My work is stuckeup here are the PDB parameters for HEME --- HETATM 3851 FE HEM 482 4.876 25.216 23.893 1.00 0.00 HETATM 3852 CHA HEM 482 5.264

RE: [gmx-users] HEME topology

Dear nirmal, try prodrg server for generating the topology file for the said pdb file. Here is the link. http://davapc1.bioch.dundee.ac.uk/prodrg/ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Nirmal

Re: [gmx-users] Coupling groups - Thermostat

Hey, In addition to the foregoing... The separate coupling is to prevent draining energy from one part to the other. It is pretty unlikely that either protein or tube will drain the other one. Water is always a different story. You can check the setup you choose afterwards, like after a short

Re: [gmx-users] Coupling groups - Thermostat

On 11/01/2012 4:23 PM, Tsjerk Wassenaar wrote: Hey, In addition to the foregoing... The separate coupling is to prevent draining energy from one part to the other. It is pretty unlikely that either protein or tube will drain the other one. Water is always a different story. You can check the

Fw: Fw: [gmx-users] trjconv in martini

- Forwarded Message - From: mohammad agha mra...@yahoo.com To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Tuesday, January 10, 2012 9:08 PM Subject: Re: Fw: [gmx-users] trjconv in martini Hi Tsjerk, I know that my question is silly but please help me. I installed python2.5

Re: [gmx-users] Hello

Dear Mark, I am facing problem in creating Heme topology...prodrg server is showing error , can you please tell how to solve this problem or can you please provide the heme topology here are the PDB coordinates for HEME

[gmx-users] failure message in GROMACS installation

  Dear All,   I am trying to install GROMACS 455. I got a series of error message in the MAKE step. Will you please take a look at the following MAKE screen file to see on how to make the installation successful?   Cheers,   Dialing   cc -DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2

[gmx-users] (no subject)

Im having problems installing Gromacs. I followed the GROMACS installation instructions as suggested by justin. But in vain. The same error is coming again and again. Please suggest. The error file is given below: /usr/bin/ld: /usr/local/lib/libfftw3.a(plan-dft-r2c-3d.o): relocation