http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
Hello GROMACS users,
I am attempting to run a molecular dynamics simulation with DNA complexed with
a small molecule. I have processed the molecule with ACPYPE, using the GAFF,
and merged the topology files into a single topology file. However, when I
attempt to use the “grompp” command
Hello,
I am using constant velocity method in order to pull a nanoparticle through a
lipid bilayer in water solution in Gromacs.
I should calculate the simultaneous force in order to take an integral over
position to obtain the PMF.
Do you know how can I measure the simultaneous force in
Dear GMX users,
I am trying to do x-ray diffraction analysis on my simulation results. I
found in the old 4.6 version, there was an option to do this under the
g_rdf module with -energy flag, but then it was removed after 5.0. The only
similar module I can find now is gmx saxs module.
I compared
Dear GMX users,
I was wondering if anyone has used the gmx densorder (originally g_densorder)
in the past utility in the past. I have system with an interface and the idea
of "
gmx densorder reduces a two-phase density distribution along an axis, computed
over a MD trajectory, to 2D surfaces
Dear gromacs user.
What should be the value of spring constant (k) and rate if
one wants to pull dsDNA (say bDNA of 16 bp ) surrounded by aqua (water
model) during pulling using umbrella sampling .
--
*With Best-Rakesh Kumar Mishra*
* (RA)CSD SINP Kolkata, India*
*E-mail -
Dear Gromacs Users,
Hi, we have added a free energy calculation of a dihedral restraint to
the free energy website. Now it has exact analytical free energy
calculations of all the restraints (can be used in absolute free
energy calculations) and the standard bonded terms
