[gmx-users] On creating pdb file using dynamic indices from g_select

Hi everyone! I intend to create a trajectory file (in pdb format) of atoms dynamically indexed by g_select. However, I failed to produce the correct pdb file. Here is how I did it. Kindle help please. 1. I created the index file using g_select for water oxygen atoms within 0.4 nm of Atom 3 g

[gmx-users] g_msd and MSD analysis

Hi everyone! I have a 20 ns  simulation (2fs timestep but coordinates saved every 0.2 ps) and I was able to calculate the mean-square-displacement of the oxygen atoms of my water solvent. The entire MSD plot looks very linear to me. I need to fit this set of MSD data to obtain the diffusion co

[gmx-users] H-bonds

Hi everyone! I tried doing H-bond analysis using g_hbond on a solute dissolved in water. The solute has hydroxyl groups. In an attempt to analyze water-bridges formed thru H-bonds, I noticed that g_hbond does not seem to give consistent results. As previously discussed in this list, I am takin

[gmx-users] option -r2 on g_hbond, a third HB citerion?

Hi everyone!   On this page http://manual.gromacs.org/online/g_hbond.html there is an option -r2 when using g_hbond. What is this r2? I can't find it in the Gromacs manual. option -a is the angle H-O-O, option -r is the O-O distance which can be switched to H-A by using the "-da no". Nee

[gmx-users] On g_hbond

Hi everyone!   On this page http://manual.gromacs.org/online/g_hbond.html there is an option -r2 when using g_hbond. What is this r2? I can't find it in the Gromacs manual. option -a is the angle H-O-O, option -r is the O-O distance which can be switched to H-A by using the "-da no". Need help

[gmx-users] On HBond definition

Hi everyone! On this page http://manual.gromacs.org/online/g_hbond.html there is an option -r2 when using g_hbond. What is this r2? I can't find it in the Gromacs manual. option -a is the angle H-O-O, option -r is the O-O distance which can be switched to H-A by using the "-da no". Need help o

Re: [gmx-users] CygWin and Gromacs 4.5.5

yes, I have also experience the same with Gromacs 4.5.5 and cygwin. I hope this issue will be addressed.Thanks From: Roland Schulz To: Discussion list for GROMACS users Sent: Wednesday, November 9, 2011 11:03 AM Subject: Re: [gmx-users] CygWin and Gromacs 4.5.

[gmx-users] Gromacs 4.5.5 installation with Cygwin

Hi everyone!   I am trying to install Gromacs 4.5.5 using Cygwin. I have succesfully compiled and installed fftw-3.2.2 according to the instructions provided below. I previously installed a Gromacs-4.5.3 using the same procedure and is still available but as a separate folder.     http://lists.g

[gmx-users] Gromacs 4.5.5 installation on Cygwin

  Hi everyone! I am trying to install Gromacs 4.5.5 using Cygwin. I have succesfully compiled and installed fftw-3.2.2 according to the instructions provided below: http://lists.gromacs.org/pipermail/gmx-users/2009-September/044792.html However, when I am at the step after running "make" (and af

[gmx-users] g_hbond

Hi everyone! I have some questions on g_hbond. According to Manual 4.5.4, hydrogen-bonds are counted/determined by g_hbond based on angle and distance cut-offs. The distance cut-off is based on the acceptor-donor distance. However, the online manual says that the distance is based on Hydrogen -

[gmx-users] g_hbond

Hi everyone! I have some questions on g_hbond. According to Manual 4.5.4, hydrogen-bonds are counted/determined by g_hbond based on angle and distance cut-offs. The distance cut-off is based on the acceptor-donor distance. However, the online manual says that the distance is based on Hydrogen -

Re: [gmx-users] placing dihedral constraints

Thanks, Justin. I'll do experiments on that.        Thu, 7/7/11, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] placing dihedral constraints To: "Discussion list for GROMACS users" Date: Thursday, July 7, 2011, 1:32 AM Mr Bernard Ramos wrote: &

Re: [gmx-users] placing dihedral constraints

/27/11, Mark Abraham wrote: From: Mark Abraham Subject: Re: [gmx-users] placing dihedral constraints To: "Discussion list for GROMACS users" Date: Monday, June 27, 2011, 5:38 PM On 06/27/2011 07:31 PM, Mr Bernard Ramos wrote: Hi! I would like to freeze two dihedrals/torsion

Re: [gmx-users] On multi-core PCs and gromacs installation

thanks for all the response. I try the suggestions. I think I ll have to do it not with fftw then. --- On Mon, 7/4/11, Mirco Wahab wrote: From: Mirco Wahab Subject: Re: [gmx-users] On multi-core PCs and gromacs installation To: gmx-users@gromacs.org Date: Monday, July 4, 2011, 11:08 PM >> I

[gmx-users] On multi-core PCs and gromacs installation

Hi everyone!   I will be installing gromacs 4.5.x in another computer but this time with four cores. The PC runs in windows and I will be using cygwin. The instructions says:   "If you want to run in parallel across a network, you need MPI. If you are running on a supercomputer you probably alrea

[gmx-users] placing dihedral constraints

Hi! I would like to freeze two dihedrals/torsion angles but allow the rest (i.e. bonds, angles) to relax during energy minimization and MD. How do I go over applying constraints? Thanks.-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] selecting atoms---MD analysis

Hi everyone!   I have already have the MD data, I need to select certain atoms/residues with their XYZ coordinates in each time frame. I have problems in using the g_select if this is the proper tool to use for this. Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs

Re: [gmx-users] Grompp error on index file

Discussion list for GROMACS users" Date: Tuesday, May 31, 2011, 10:09 AM Mr Bernard Ramos wrote: > Hi everyone! >  I added a residue on the gromacs 4.5.3 I have. I followed the instructions >as indicated in the "Adding A Residue to a Force Field" with this link >

[gmx-users] Grompp error on index file

Hi everyone!   I added a residue on the gromacs 4.5.3 I have. I followed the instructions as indicated in the "Adding A Residue to a Force Field" with this link http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field?highlight=adding+residue. I added the residue to residu

Re: [gmx-users] On posre.itp

I think I've got the answer. It is on the input pdb file. The heavy atoms need to be labeled properly. thanks --- On Sat, 5/7/11, Mr Bernard Ramos wrote: From: Mr Bernard Ramos Subject: Re: [gmx-users] On posre.itp To: "Discussion list for GROMACS users" Date: Saturday, May 7

Re: [gmx-users] On posre.itp

them. Thanks.     --- On Sat, 5/7/11, Mark Abraham wrote: From: Mark Abraham Subject: Re: [gmx-users] On posre.itp To: "Discussion list for GROMACS users" Date: Saturday, May 7, 2011, 5:10 PM On 7/05/2011 7:01 PM, Mr Bernard Ramos wrote: Hi everyone!   I was able to generate

[gmx-users] On posre.itp

Hi everyone!   I was able to generate a pdb file in which the hydrogens for the molecule are already included (that way I avoided using the hdb file for the pdb2gmx). However, when I checked the posre.itp, the some of the restraints were applied to the hydrogens. Is this correct because I am not

Re: [gmx-users] RTP file formats

Thanks for the response. We will be using the CHARMM ff. --- On Thu, 5/5/11, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] RTP file formats To: "Discussion list for GROMACS users" Date: Thursday, May 5, 2011, 8:38 PM Mr Bernard Ramos wrote: >

[gmx-users] RTP file formats

Hi everyone!   The *.rtp file formats we have on Gromacs rtp file exmaples do not necessarily have the [dihedrals] or [impropers] part. They normally only have the [atoms] and [bonds]. In fact, the [bonds] section do not enumerate the constants or parameters. This is not what is written or shown

[gmx-users] Urey-Bradley constant in CHARMM to GMX

The Urey Bradley constant in CHARMM is expressed in units of kcal per (mol squared angstrom). However, in the Gromacs manual in Table 5.5, it is expressed in kJ/mol. How do we convert the constant from kcal per (mol squared angstrom) to kJ/mol in gromacs. Could gromacs have been expressing this

[gmx-users] 1,5 and 1,6 LJ interactions for OPLS AA SEI

Hi everyone!   The OPLS AA SEI for carbohydrates scales the 1,5 and 1,6 interaction by a certain factor. How do I go about introducing the scaling of these intearctions in the ff parameters? The CHARMM ff also has certain 1,4 parameters, I am not sure how we can go about placing these specific p

[gmx-users] On dihedral type for CHARMM

Hi everyone!   I am currently studying CHARMM ff and I have a question on the functional type of the CHARMM dihedral. On the ffbonded.itp, the function type for CHARMM dihedrals is 9. However, this functional type is not listed on Table 5.5 of the manual. I read that there are 9 supported funct

Re: [gmx-users] on force fields

ers" Date: Monday, February 21, 2011, 10:41 AM Mr Bernard Ramos wrote: > Thanks for the reply on my first querry. I have another one. If I add a NEW > atom type in *.atp file, will Gromacs automatically recognize this atom > type?    Theoretically, yes, provided that you supply any

Re: [gmx-users] on force fields

list for GROMACS users" Date: Wednesday, February 16, 2011, 1:53 PM On 16/02/2011 3:41 PM, Mr Bernard Ramos wrote: Hi everyone!   I need to update the gromos force field 53A6 with the new force field 53ACARBO (JCC 10 NOV 2010).   1. I will have to change the parameter values i

[gmx-users] on force fields

Hi everyone!   I need to update the gromos force field 53A6 with the new force field 53ACARBO (JCC 10 NOV 2010).   1. I will have to change the parameter values in the file ff_bonded.itp and ff_nonbonded.itp in the gromos53a6.ff. Are these the only files that I need to update if I need to switc

Re: [gmx-users] luck

day, February 2, 2011, 2:32 AM Mr Bernard Ramos wrote: > > this is the command i am using: >  pbd2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce > then I choose a force fileld. > then I get the error and no new files generated at all. >  My working directory is: >

Re: [gmx-users] luck

: From: Justin A. Lemkul Subject: Re: [gmx-users] luck To: "Discussion list for GROMACS users" Date: Wednesday, February 2, 2011, 2:15 AM Mr Bernard Ramos wrote: > Hi! >  I am actually following your lysozyme tutorial. I ve been using different >pdb files including that

Re: [gmx-users] luck

4.5.3 Source code file: futil.c, line:491   File input/output 1AKI.pdb For more etc -- --- On Mon, 1/31/11, Mr Bernard Ramos wrote: From: Mr Bernard Ramos Subject: Re: [gmx-users] luck To: jalem...@vt.edu, "Discussion list for GROMACS users&q

Re: [gmx-users] luck

--- On Mon, 1/31/11, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] luck To: "Gromacs Users' List" Date: Monday, January 31, 2011, 12:33 PM Mr Bernard Ramos wrote: > Do I need to type in g_luck instead? > Typing an email and waiting for a re

Re: [gmx-users] luck

wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] luck To: "Discussion list for GROMACS users" Date: Monday, January 31, 2011, 12:11 PM Mr Bernard Ramos wrote: > Hi everyone! >  I have two questions. >  1. after I installed gromacs 4.5.3 and "which mdr

Re: [gmx-users] luck

Do I need to type in g_luck instead? --- On Mon, 1/31/11, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] luck To: "Discussion list for GROMACS users" Date: Monday, January 31, 2011, 12:11 PM Mr Bernard Ramos wrote: > Hi everyone! >  I have two

[gmx-users] luck

Hi everyone!   I have two questions.   1. after I installed gromacs 4.5.3 and "which mdrun" was able to give the correct path, I was not able to run "luck". Instead, "luck" gives an error "command not found". Is this ok? What went wrong? Do I need to install again gromacs?   2. I tried doing "pd

[gmx-users] Installing Gromacs with Cygwin

Dear all, I need help. I am trying to install Gromacs using Cygwin. However, I do not seem to have access to it. I am very new with Cygwin. I just followed the steps provided by the following sites:  http://machine-phase.blogspot.com/2009/04/how-to-install-gromacs-on-windows-vista.html and http: