Dear Chris
Thank you very much for giving your comprehensive information on my mdp
options.
In my current simulation, I am trying to switch off coulombic interactions
while keeping VDW on.
In gromacs manual, it is mentioned that with parallel simulations and/or
non-bonded force calculation on the
Thank you everyone for your reply.
I have resolved the problem for reply of Justin from previous mail at gmx
list.
Thank you Justin again
On Thu, Mar 16, 2017 at 5:57 PM, Amir Zeb wrote:
> You probably follow umbrella sampling for free energy calculation.
> If it is so,
You probably follow umbrella sampling for free energy calculation.
If it is so, you may change the position of your drug.itp file in topology
file, means that before the protein topology.
I hope this might solve your problem.
Good luck!
Amir
On Thu, Mar 16, 2017 at 2:49 AM, Tasneem Kausar
On 3/16/17 5:49 AM, Tasneem Kausar wrote:
Dear All
I am trying to perform free energy calculations of a protein drug system.
I am using Gromacs-5.1.4 for this purpose. decoulpe molecule type i.e. drug
molecule is defined in separate drug.itp file. From the discussions of
mailing list I have
As article name in reference says PLUMED can be used for free-energy
calculations with molecular dynamics.
On Thursday, March 16, 2017 1:23 PM, Hannes Loeffler
wrote:
On Thu, 16 Mar 2017 10:09:58 +
Vytautas Rakeviius wrote:
>
On Thu, 16 Mar 2017 10:09:58 +
Vytautas Rakeviius wrote:
> You should try to add PLUMED (plumed.org) to GROMACS for such
> things.Bonomi, M., Branduardi, D., Bussi, G., Camilloni, C., Provasi,
> D., Raiteri, P., ... & Parrinello, M. (2009). PLUMED: A portable
> plugin
I can't help you much because I have not really paid attention how
restraints in alchemical free energy simulations are handled in newer
versions of Gromacs. I understand that [intermolecular_interactions]
is a new section that allows using restraints based on global indices.
The error message
You should try to add PLUMED (plumed.org) to GROMACS for such things.Bonomi,
M., Branduardi, D., Bussi, G., Camilloni, C., Provasi, D., Raiteri, P., ... &
Parrinello, M. (2009). PLUMED: A portable plugin for free-energy calculations
with molecular dynamics. Computer Physics Communications,
On 10/16/14 9:57 AM, elham tazikeh wrote:
Dear Justin
when I am doing this tutorial
*sh mklambdas.sh run.mdp topol.top equil.gro*
I got following error:
*mklambdas.sh: 12: mklambdas.sh: Syntax error: ( unexpected*
How can I fix this?
Well, apparently there's a syntax error in the