Re: [gmx-users] Is the Amber14sb ff on the gromacs website actually amber14sb force field

​Hi,​ On Mon, Jun 25, 2018 at 8:20 AM Evelyne Deplazes < evelyne.depla...@curtin.edu.au> wrote: > Hi gromacs users > > When doing pdb2gmx using the Ambersb14 download from the gromacs force > field website ( > http://www.gromacs.org/Downloads/User_contributions/Force_fields) it is > labelled

[gmx-users] Is the Amber14sb ff on the gromacs website actually amber14sb force field

Hi gromacs users When doing pdb2gmx using the Ambersb14 download from the gromacs force field website (http://www.gromacs.org/Downloads/User_contributions/Force_fields) it is labelled Amber99sb-ILDN and the reference matches the amber99sb_ILDN force field. Is the file downloaded from the

[gmx-users] Distance vector file for g_analyze: incompatibility of normal and vector

Dear All, I want to generate the autocorrelation function for end-to-end distance vector of my peptide and using g_dist, I have generated a dist.xvg file. On giving this file as input to g_analyze and giving the option -P 1 (for Legendre polynomial), it gives the error: "Incompatible mode bits:

Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

update: I am trying using the way that you have suggested me # the first step gmx convert-tpr -s old.tpr -o new.tpr -extend 5 mdrun_mpi -s new.tpr -deffnm old -cpi old -append Here there is an issue: Each time all pieces of the files will be merged into "old" (.trr .edr and .cpt). But

Re: [gmx-users] Implicit solvent

Hi, Implicit solvation works with multiple threads in GROMACS 4.5.x, but has been broken ever since (and will be removed in GROMACS 2019). So I suggest you use 4.5.7, or some other software (e.g. AMBER) Mark On Sun, Jun 24, 2018 at 4:00 AM Chhaya Singh wrote: > I am running implicit solvent

Re: [gmx-users] implicit solvent error

sorry i attached a wrong file. this is my inputs about the implcit solvent integrator = md dt = 0.005; ps ! nsteps = 2000 ; total 10 ns. nstlog = 5000 nstxout = 0 ;1000 nstvout = 0 ;1000

Re: [gmx-users] increasing md run speed

Hi, You might be, but you need to look at the bottom of the log files for performance feedback. What is common and different? Mark On Sun, Jun 24, 2018 at 6:23 AM neelam wafa wrote: > Hi, I have run a 100 ps simmulation of the same protein with different > ligand and its producing

Re: [gmx-users] implicit solvent error

Your EM is unrelated to dynamics. I mean, it could, but we don't know anything about your simulated system. I am of course assuming that your MPI setup is optimal for gmx and you actually get to use those 16 threads, assuming those aren't an emulation of some sort. On 6/24/2018 1:33 AM,

Re: [gmx-users] implicit solvent error

Hi, I have attached the energy minimization mdp file. please look through it . cpp = /lib/cpp ; prepocessor of the current machine define = -DFLEXIBLE ; -DPOSRES,

Re: [gmx-users] implicit solvent error

This input has no information about implicit solvent and a simple google search immediately yields mdp examples using gbsa. As far as performance is concerned, we don't know the specs of your machine or the size of your system. With cutoff electrostatics and a cutoff of 5 nm, one can expect

[gmx-users] implicit solvent error

Hi, I am trying to simulate a protein in an implicit solvent in groamcs using amber ff99sb ildn . the mdpfile that I am using is I have shown below: integrator = md dt = 0.001 ;0.005; ps ! nsteps = 500 ; total 5 ns. nstlog =