Re: [gmx-users] Error in free energy calculation (Chris Neale)

2020-03-23 Thread Sadaf Rani
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

Re: [gmx-users] Error in free energy calculation

2017-03-16 Thread Tasneem Kausar
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,

Re: [gmx-users] Error in free energy calculation

2017-03-16 Thread Amir Zeb
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

Re: [gmx-users] Error in free energy calculation

2017-03-16 Thread Justin Lemkul
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

Re: [gmx-users] Error in free energy calculation

2017-03-16 Thread Vytautas Rakeviius
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: >

Re: [gmx-users] Error in free energy calculation

2017-03-16 Thread Hannes Loeffler
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

Re: [gmx-users] Error in free energy calculation

2017-03-16 Thread Hannes Loeffler
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

Re: [gmx-users] Error in free energy calculation

2017-03-16 Thread Vytautas Rakeviius
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,

Re: [gmx-users] error in free energy calculation

2014-10-16 Thread Justin Lemkul
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