[gmx-users] gmx dipoles and gmx potential output files detail

in detail. Thanks in advance Mahender singh -- 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 http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] umbrella sampling and PMF calculation by using pull-geometry=direction in gromacs 5.0.4

in the umbrella sampling parameters. Can you provide me some suggestion on this topic. Thanks in advance for help. with regards Mahender Singh Hello good morning to all I did steered md simulation by using following code ;pull code pull= umbrella pull_geometry= direction

[gmx-users] umbrella sampling and PMF calculation by using pull-geometry=direction in gromacs 5.0.4

something wrong with the parameters or understanding the PMF curve wrongly. can any one give their suggestion on this. thanks in advance of user time and help. with regards Mahender Singh -- Gromacs Users mailing list * Please search the archive

Re: [gmx-users] Problem in installation

with good wishes Mahender singh Science student -- 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 http://www.gromacs.org/Support

Re: [gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

the expected graph as there will be increase in the force when drug will enter in the membrane. Can you kindly comment of the statement. with regards Mahender Singh Thank you dear Justin and Christopher Neale for your help. Solute is at -z relative to the bilayer and wants to pull toward +z from

Re: [gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

understood the parameters wrongly), and from this simulation I want to do the umbrella sampling for free energy calculation. with regards Mahender Singh Hi Christopher Neale and Justin I used now following pull code (what i understood from the previous emails) to pull the drug across

Re: [gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

? with regards Mahender singh Dear Justin: I think you are correct. It may not even really be that much of a hassle though one may need to be very careful in system setup for umbrellas near the center of the bilayer when using pull_start=yes rather than

[gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

of the pull and reference group during the smd simulation, am I correct? thanks in advance, for any help, comments or suggestions. with regards Mahender singh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support