Re: [gmx-users] SASA calculation for one replica in REMD

The trajectory output from GROMACS is specific to that specific ensemble, in your case at given temperature. So each individual trajectory is for a given temperature. And that sounds like it is exactly what you want. If you want to follow the trajectory for a single replica, that's when it gets

Re: [gmx-users] SASA calculation for one replica in REMD

Dear Gromacs Users, Thank you for all suggestions. Yes I can use gmx SASA, but I want to know how do we use that in REMD simulations? Specifically, I want to calculate SASA for molecules in my first replica (298 K). But I think the trajectory in the first replica contains the information

Re: [gmx-users] Average rmsd

Ok i ll try Thanks On Mon, 29 Apr 2019, 7:06 am Neena Susan Eappen, < neena.susaneap...@mail.utoronto.ca> wrote: > Hi Neelam, > > I do not have Xmgrace tool, but you can open up the xvg file on excel and > calculate average. > -- > Gromacs Users mailing list > > * Please search the archive at >

Re: [gmx-users] Average rmsd

Hi Neelam, I do not have Xmgrace tool, but you can open up the xvg file on excel and calculate average. -- 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

[gmx-users] RMSD command line doubt

Hello gromacs users, My goal is to calculate all-atom rmsd of every structure in the trajectory(.trr) to the final structure after simulation (.gro). Q1) So, I don't understand the purpose of giving .tpr input file (which was the input structure file before production mdrun) as a structure

[gmx-users] Assertion failed: Condition: ic->coulomb_modifier == eintmodEXACTCUTOFF

Hi, I am using Gromacs 2018.6 to run a simulation of dppc lipids and the input file is as follows. 26 cutoff-scheme = Verlet 27 verlet-buffer-tolerance = -1; set rlist manually 28 nstlist = 10 29 ns-type = grid 30 pbc = xyz 31 rlist