[gmx-users] Question

Hi!! I am changing my equipment for a AMD quad Core with two physical processors and would like to know if in this configuration I will have problems of compatibility with gromacs 4.0. Elias Silva ___ gmx-users mailing listgmx-users@gromacs.org htt

[gmx-users] genion

Hi!! I want know because we must neutralize the total load of the system (protein + water) into of the box with genion. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at htt

[gmx-users] genion

Hi!! I want know because we must neutralize the total load of the system (protein + water) in the interior of the box with genion. Elias ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search t

[gmx-users] question energy

Hi, users of the Gromacs. I have a question for you. I want to know which the meaning of the term (14) in the energies Coulomb 14 and Lenard Jones 14. thanks ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/

[gmx-users] Queston about energy

Hi! I made the molecular dynamics of a peptideo and now I want to make the analysis of energies. Thus which the meaning of the long energy of Coulomb of and short reach? The same question valley for the energies gotten for Lenard Jones (LR, SR.)? Elias _

[gmx-users] question

Dear users!!! Anybody can significate of energy Lj -14, LJ -LR Coulomb- SR and LR? Elias ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the

[gmx-users] g_energy and/or g_enemat

Hi, I have doubts in as to use g_energy and/or g_enemat to calculate the free energy of a molecule (1JNR.pdb)reductase of the APS. I made two dynamic the temperatures of 300K and 311K.Waht´s the best option enters these two programs for the calculation? The calculated energy is stabilization energ

[gmx-users] g_energy and g_enemat

Hi, I have doubts in as to use g_energy and/or g_enemat to calculate the free energy of a molecule (1JNR.pdb)reductase of the APS. I made two dynamic the temperatures of 300K and 311K.Waht´s the best option enters these two programs for the calculation? The calculated energy is stabilization energ

[gmx-users] potential oxiredution

Hi!!  I have a question for you... Some way to calculate the oxiredution potential (ORP) using the Gromacs package?   Elias ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscri

[gmx-users] bonds

Hi! I have a question . I am working with a protein that they will count twocenters FES co-ordinated for cisteins, these cisteins were not on to ironatoms, thus I modified the archive itp only with respect the bonds, no angles or diedrals, to bind to these two residuos. After the minimização, Imade

[gmx-users] Bonds

Hi!  I have a question . I am working with a proteina that they will count two centers FES co-ordinated for cisteins, these cisteins were not on to iron atoms, thus I modified the archive itp only with respect the bonds, no angles or diedrals, to bind to these two residuos. After the minimização, I

[gmx-users] edit specbond.dat file

Message: 2Date: Tue, 15 Aug 2006 13:05:07 -0300From: "Elias santos" <[EMAIL PROTECTED] >Subject: [gmx-users] clusters [4Fe-4S]+2To: gmx-users@gromacs.orgMessage-ID:       < [EMAIL PROTECTED]>Content-Type: text/plain; charset="iso-8859-1"Hi !!I to construct to the

[gmx-users] conections Fe-S(Cys)

Hi  As I fill the fields of the archive specbond.dat for linkings between atoms of Fe of residue FS4 and SG of residuo of cystein Elias ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post

[gmx-users] clusters [4Fe-4S]+2

Hi !! I to construct to the block for residuo FS4 of the two clusters in the  .rtp file of the force field ffgmx with all the linkings, angles etc., beyond the on and not on parameters. When I run pdb2gmx, it does not give menssagem of error, but the linkings between the cysteins (SG) and atoms of

[gmx-users] The file

HI! I have a problem.  I am working with a molecule that will count two clusters, co-ordinated for cysteins. But in the pdb file does not exist linkings between iron atoms and of the cystens, even so literature affirms that it exists. How I can edit this file?  Therefore when I edited it even s