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Hello Users
I am beginner for gromacs
1)i need to ask if i am changing my ref_t more or less than 300K then i need to change the gen_temp as well
2) During the energy minimization, nvt.mdp and npt.mdp: the rlist, rvdw and rcoulomb should be same
so here is my npt.mdp file
; VARIOUS PREPROCESSING OPTIONS
title = NPT simulation (constant number, pressure and temperature)
cpp = /usr/bin/cpp
define = -DPOSRES
; RUN CONTROL PARAMETERS
integrator = md
dt = 0.002
nsteps = 1000000
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no ; Assign velocities to particles by taking them randomly from a Maxwell distribution
gen_temp = 300 ; Temperature to generate corresponding Maxwell distribution
gen_seed = 135962 ; Seed for (semi) random number generation.
; OPTIONS FOR BONDS
constraints = h-bonds
constraint-algorithm = lincs
continuation = yes
shake-tol = 0.0001
please resolve the problem
i) regarding velocity generation, if you are generating velocities I would do it by using the same temperature as the thermostat. It’s not a huge deal in principle, as the thermostat will correct a wrong set of starting velocities very quickly, but anyway I would use the same.
Also please note this
gen_vel = no ; Assign velocities to particles by taking them randomly from a Maxwell distribution
gen_temp = 300 ; Temperature to generate corresponding Maxwell distribution
gen_seed = 135962 ; Seed for (semi) random number generation.
Here you are not generating velocities as you set gen_vel = no, so the gen_temp should be ignored. For gen_seed I would leave -1 as this is the most robust way to have random velocity generation, except if you want a specific seed for some reason.
ii) This is a statement more than a question. I never head that they should be the same, let alone during EM, but I might be wrong. My understanding is that the vdW and Coulomb radii depend (at least) on the force field implementation. I think rlist should be at least as long as the longest of the two radii, but it’s irrelevant as it is then fine tuned automatically by GROMACS depending on some internal parameters like your hardware.
On a more general note, a few details of your mdp depend on the force field, so I would check previous literature to use the same parameters. I would also switch the barostat to the c-rescale.
Thanks for your valuable time
I have queries, that for nvt, npt or for mdrun the ref_temperature and the gen_temperature should be same
if ref_298.15 then gen_temp should be same as ref_temperature or it should be 300k (for nvt,npt and mdrun) as in gromacs manual, gen_ temp 300k (maxwell distribution) it is mention over there
i need to ask to match the experimental density what should be done after equilibrium , it should be npt first then nvt or nvt first then npt
The temperature you should use is the temperature you want to use, not the one reported on GROMACS manual, that is an example. If you want to run at the “standard” room temperature, then you should set both the generation and the reference to 298.15K (although I wouldn’t expect it to matter that much with respect to 300K). If you need to run at other temperatures, you set the mdp to those temperatures.
Regarding the density, generally that is experimentally calculated at a given temperature and a given pressure. I would go with NVT at that T, then NPT at that T and that P. After a few ns (depending on the system dimension and composition) you will have an equilibrated box from which you can calculate the density.
Thanks for reply
Actually I am doing md simulation of ethylene glycol with choline chloride to match the actual density reported in experimental paper, but actual i am not getting any idea to pack how much molecules need to pack in packmol?
if you have any idea or calculation to acheiving the density and how much amount of molecules should be added?
please resolve the issue