[gmx-users] Re: 1-4 interactions free energy calculations

. As soon as I start my tests, I will let you know. Thank you for the guidance, Sonia Aguilera Graduate Assistant Department of Checmical Engineering Universidad de los Andes -- View this message in context: http://gromacs.5086.x6.nabble.com/1-4-interactions-free-energy-calculations

[gmx-users] Re: 1-4 interactions free energy calculations

help in any aspect if I neutralize the system? Thank you very much in advance, Best regards, Sonia Aguilera Graduate Assistant Department of Chemical Engineering Universidad de los Andes -- View this message in context: http://gromacs.5086.x6.nabble.com/1-4-interactions-free-energy

[gmx-users] 1-4 interactions free energy calculations

the expansion of the constraint coupling matrix lincs-order = 12 Thank you in advance!! Sonia Aguilera Graduate assistant Chemical Engineering Department Universidad de los Andes -- View this message in context: http://gromacs.5086.x6.nabble.com/1-4-interactions-free-energy-c

[gmx-users] Parallelization performance

e C-H bonds here ; Type of constraint algorithm constraint-algorithm = lincs ; Do not constrain the starting configuration continuation = no ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 Thanks in advance! Sonia Aguilera Gra

[gmx-users] Re: BAR histogram results

foreign_lambda = 0.1 0.5 Does it mean that I have to repeat my simulations for 0.1 and 0.5 so that they can have foreign lambda 0.3? Thank you, Sonia Aguilera -- View this message in context: http://gromacs.5086.n6.nabble.com/BAR-histogram-results-tp5005095p5006125.html Sent from the

[gmx-users] Re: Error: The Y-size of the box times the triclinic skew factor is smaller than the number of DD cells times the smallest allowed cell size

Thank you Justin, So, your advice is not to perform the npt calculation and to run the md after the nvt? Thank you, Sonia Aguilera -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-The-Y-size-of-the-box-times-the-triclinic-skew-factor-is-smaller-than-the-number-of

[gmx-users] Error: The Y-size of the box times the triclinic skew factor is smaller than the number of DD cells times the smallest allowed cell size

order = 12 Can you please tell my what is wrong? I runned previous nvt, npt and md simulation with the same box size and protein but in water. Is there any way of solving this problem without affecting the accuracy of the simulation? Thank you in advance Sonia Aguilera -- View

[gmx-users] BAR histogram results

on the tutorial, something is wrong with my sampling. I have been trying to understand Bennett's paper, but I have not been successful. Can someone explain to me the meaning of the values in each axis? How should I interpret this data? What can I do to improve my sampling? Thank you in adva

[gmx-users] Re: Error There is no domain decomposition for 6 nodes that is compatible

ioning free-energies of relatively large molecules, where the intra-molecular non-bonded interactions might lead to kinetically trapped vacuum conformations. Again, I don't understand what is the real meaning of that. Can you please make this clear for me? Thank you again, Sonia Ag

[gmx-users] Error There is no domain decomposition for 6 nodes that is compatible

log and mdp file. mdp_and_log_files.zip <http://gromacs.5086.n6.nabble.com/file/n5001648/mdp_and_log_files.zip> Thank you in advance, Sonia Aguilera Graduate Assistant Universidad de los Andes-Colombia -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-There-is-no-domain-decompos

[gmx-users] Re: Notes and warnings using grompp

I don´t know what to change or where. Should I ignore the note? I have seen (second note) that since it is just a note, it can be ignored, but according with the parameters of the note, what do you think? Thank you, Sonia Aguilera -- View this message in context: http://gromacs.5086.n6

[gmx-users] Re: Topology and mdp file for coupling vdw and coulombic interactions for running FE calculations using BAR

zero with the same settings in the mdp file. Can you please make this clear for me? Should I use the topoly file with the original charges for both calculations? Thank you, Sonia Aguilera Graduate Student-Chemical Engineering Department Universidad de los Andes Colombia -- View this message in