[gmx-users] Scd

Dear Justin,I want to obtain the error bar for deuterium order parameter (Scd). what command must i use for it?regards,Mr.Ganj -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] Error in number og H-bond

Dear Justin,I calculated the H-bond with g_hbond. I want to calculate the error of H-bond, what must i do?many thanks,Mrs. Mahdavi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] forcefield parameter for bromide ion

Hi I need to do a simulation of protein in presence of LiBr salt solution. However, I am not finding any force field parameters for bromide ion either in charmm forcefields or amber forcefields. Can someone suggest a decent source for bromide ion forcefield parameters that one could employ in

Re: [gmx-users] GPU installation of gromacs:Tesla K20c

1) put `source /usr/local/gromacs/bin/GMXRC` in your ~/.bashrc file. 2) Type `echo $PATH` and make sure you find your path to Gromacs in there. 3) try `gmx mdrun`. Im not sure whether that is already required for Gromacs 5.0.5. Also, have a look in /usr/local/gromacs/bin to see whether 'gmx',

Re: [gmx-users] dihedral calculation

On 10/9/15 6:06 PM, Parvez Mh wrote: Dear all, I want to measure dihedral angle of a particluar dihedral over all time steps. I see in gromacs that g_angle can calculate the distribution of dihedral but not the exact angle measurement. Is there any option in gromacs to measure dihedral over

[gmx-users] dihedral calculation

Dear all, I want to measure dihedral angle of a particluar dihedral over all time steps. I see in gromacs that g_angle can calculate the distribution of dihedral but not the exact angle measurement. Is there any option in gromacs to measure dihedral over the all time steps. Thanks Masrul --

Re: [gmx-users] dihedral calculation

Thanks Dr. Lemkul Regards Masrul On Fri, Oct 9, 2015 at 5:08 PM, Justin Lemkul wrote: > > > On 10/9/15 6:06 PM, Parvez Mh wrote: > >> Dear all, >> >> I want to measure dihedral angle of a particluar dihedral over all time >> steps. I see in gromacs that g_angle can calculate

Re: [gmx-users] Virtual sites error

This looks very strange that from the whole assortment of the molecules in the force field only a humble methyl group in thymine lacks proper definition causes such an error. Even nucleotides which I added myself to the force field files don't produce any errors Is there any way to remedy

Re: [gmx-users] forcefield parameter for bromide ion

If you are not restricted to the Amber or charmm force-fields for your protein, I believe OPLS-AA has Br- anions. Note that ions in traditional (non-polarizable) force fields are far from perfect so be careful when simulating with them if you concentration is above a few hundred millimolar.

Re: [gmx-users] Confusion on improper dihedrals and Urey-Bradley (lost when converting from Amber with acpype)

On 10/8/15 11:48 AM, Nicolas Cheron wrote: Dear all, I am joining a project where people are using the CHARMM22 force field. They converted a .prmtop file from Amber to Gromacs format with acpype. In the output topology, there are no Urey-Bradley potentials or improper dihedrals (for example,

Re: [gmx-users] Virtual sites error

If memory serves me right, the atom type for the carbon in the thymine ring lacks default constraint lengths to the dummy masses. That combination of atom types are not used for aminoacids. You will need to calculate what constraint lengths yield the correct geometry for the CH3-group, which is