Re: [gmx-users] Gromos DPPC bilayer: different results for 4.0.7 and 4.6.5

2013-12-24 Thread Szilárd Páll
Just wondering, has anybody done a comparison with the Verlet scheme? It could be useful to know whether it produces results consistent with the 4.6 group scheme implementation or exhibits different behavior. Cheers, -- Szilárd On Sun, Dec 22, 2013 at 1:08 AM, Lutz Maibaum

Re: [gmx-users] Potential energy calculations

2013-12-24 Thread virk
Justin Lemkul wrote Gromacs reports energies in kJ per mole of equivalent systems. If you're looking for a value like configurational energy, use g_energy -nmol as needed to divide by the number of molecules in the system. -Justin On Mon, Dec 23, 2013 at 8:49 PM, virk lt; virkblitz@

[gmx-users] GridMAT-MD gnuplot

2013-12-24 Thread shahab shariati
Dear gromacs users I used GridMAT-MD to obtain area per lipid and bilayer thickness. I used vector for output_format in param_example file. Based on the user guide for GridMAT-MD, when I used gnuplot: perl convert_to_gnuplot.pl output.frame1.20x20.average_thickness.dat 20 20 I encountered

Re: [gmx-users] GridMAT-MD gnuplot

2013-12-24 Thread Justin Lemkul
On 12/24/13, 9:59 AM, shahab shariati wrote: Dear gromacs users I used GridMAT-MD to obtain area per lipid and bilayer thickness. I used vector for output_format in param_example file. Based on the user guide for GridMAT-MD, when I used gnuplot: perl convert_to_gnuplot.pl

Re: [gmx-users] Calculating the displacement of an atom QUERY

2013-12-24 Thread Justin Lemkul
On 12/24/13, 2:38 AM, rbbioinfo wrote: Hi, I want to plot the total displacement of an atom/ion along Z axis with respect to time. Anybody kindly help me regarding how to calculate the movement of any atom using gromacs. An early response will be highly appreciated. Sounds like a job for

[gmx-users] bug in aminoacids.c.tdb (gromos 54a7) ?

2013-12-24 Thread fciocco
Hi, I'm not sure if this is a bug, but I have noted that in aminoacids.c.tdb (gromos 54a7 FF) two different dihedrals are defined for the same set of atoms: for [ COO- ] C-termini: [ dihedrals ] N CA C O2 gd_45 N CA C O2 gd_42 and for [ COOH ]: [

Re: [gmx-users] bug in aminoacids.c.tdb (gromos 54a7) ?

2013-12-24 Thread Tsjerk Wassenaar
Hi Facundo, This is intended. The actual dihedral is a combination of two simpler types. Cheers, Tsjerk On Tue, Dec 24, 2013 at 8:07 PM, fciocco fcio...@gmail.com wrote: Hi, I'm not sure if this is a bug, but I have noted that in aminoacids.c.tdb (gromos 54a7 FF) two different dihedrals

[gmx-users] pdb2gmx gives topol.top without values for bonds angles and dihedrals.

2013-12-24 Thread David Saez
Dear all, I want to create a topology for S-adenosylmethionine using AMBER99SB force field. I had to create some new atomtypes and, accordingly, I have modified all the necessary files (atomtypes.atp, ffbonded, ffnonbonded, etc). When I make pdb2gmx -f sam.pdb I obtain a topol.top describing

Re: [gmx-users] pdb2gmx gives topol.top without values for bonds angles and dihedrals.

2013-12-24 Thread David Saez
Thank you very much Justin for your quick answer. Greetings -- View this message in context: http://gromacs.5086.x6.nabble.com/pdb2gmx-gives-topol-top-without-values-for-bonds-angles-and-dihedrals-tp5013521p5013524.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. --