[gmx-users] simulation of two peptides

Hello, What are the necessary steps to set up and run a simulation of two peptides? Thank you in advance, Michael Owen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscrib

[gmx-users] TFE-water minimization

Hello, I have created my own TFE.itp file for a mixed solvent simulation containing TFE and TIP4P water. To test my TFE file I put one TFE molecule in a box of solvent and and tried to minimize it using the following parameters: define = -DPOSRES cpp = /lib/cp

[gmx-users] mixed solvent energy minimization

Title: mixed solvent energy minimization Hello Gromacs Users; I am trying to equilibrate a box that contains TFE and TIP4P water molecules using the OPLSAA/L force field. The system converged several times using the steepest descent method during energy minimizations, but each time I attempte

[gmx-users] mixed solvent minimization

Title: mixed solvent minimization Hello Gromacs Users, I am trying to equilibrate a box that contains TFE and TIP4P water molecules using the OPLSAA/L force field.  The system converged several times using the steepest descent method, but each time I attempted a full simulation I received th

[gmx-users] no coordinates in .top file

Sincerely, Michael Owen Message: 1 Date: Tue, 10 Oct 2006 16:59:26 +0200 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] RE: no coordinates in .top file To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; char

[gmx-users] RE: no coordinates in .top file

for any suggestions. Michael Owen Message: 1 Date: Tue, 10 Oct 2006 00:12:01 +0200 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] no coordinates in .top file To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; c

[gmx-users] no coordinates in .top file

Title: no coordinates in .top file Fellow gmx users, I made a tolopgy file for TFE in water  by "hand" for the OPLSAA/L force field to be used in a simulation containing a mixed solvent.  I made a similar TFE.itp file and included it in the mixed solvent topology file.  when I ran grompp be

[gmx-users] creating topology files

Title: creating topology files Fellow gmx users, I am trying to create a topology file for TFE using the olpsaa/l force field to simulate a peptide in a mixed solvent.   I created a molecule.itp file (as it was suggested in the manual), a molecule.gro file for TFE and I was able to place the

[gmx-users] distance restraints: -merge

Title: distance restraints: -merge Fellow gmx-users, I would like to constrain the distance of an ion to specific atoms of a protein.  I recently read a message in which the use of the option -merge in the pdb2gmx program was suggested.  How can I use this option to form these constraints?

[gmx-users] VAL group

Title: VAL group Hello  fellow gmx users, when I convert a pdb file of a peptide that contains a valyl residue into a .gro file a separate "group" is made for the atoms in the valyl residue.  This has happened when OPLSAA/l and the GROMOS96 53a6 force fields were used.  The molecule appears

[gmx-users] VAL group

Title: VAL group Hello  fellow gmx users, when I convert a pdb file of a peptide that contains a valyl residue into a .gro file a separate "group" is made for the atoms in the valyl residue.  This has happened when OPLSAA/l and the GROMOS96 53a6 force fields were used.  The molecule appears

[gmx-users] VAL group

Title: VAL group Hello gmx users, when I convert a pdb file of a peptide that contains a valyl residue into a .gro file a separate "group" is made for the atoms in the valyl residue.  This has happened when OPLSAA/l and the GROMOS96 53a6 force fields were used.  The molecule appears as one

[gmx-users] help with distance restraints

Title: help with distance restraints Hello, I am trying to use NMR restraints to position a Cu2+ ion around specific residues of a peptide.  I added Cu2+ using "genion" and then initiated "grompp" before an energy minim minimization.  I received the following error message while executing "

[gmx-users] Distance restraints

Title: Distance restraints Hello, I am trying to use NMR restraints to position a Cu2+ ion around specific residues of a peptide.  I added Cu2+ using "genion" and then initiated "grompp" before an energy minim minimization.  I received the following error message while executing "grompp":