# Drude ff for polymers

**URL:** https://gromacs.bioexcel.eu/t/drude-ff-for-polymers/2420
**Category:** User discussions
**Created:** [June 28, 2021, 11:27am UTC](https://gromacs.bioexcel.eu/t/drude-ff-for-polymers/2420 "2021-06-28T11:27:04Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![NLi](https://avatars.discourse-cdn.com/v4/letter/n/c57346/32.png) [@NLi](https://gromacs.bioexcel.eu/u/NLi)
#### Post date: [June 28, 2021, 11:27am UTC](https://gromacs.bioexcel.eu/t/drude-ff-for-polymers/2420/1 "2021-06-28T11:27:04Z")

</div>

Hi. I have been trying to use Drude ff to simulate PEG-water solution. I have installed the Drude-compatible Gromacs following the instructions on [MacKerell Lab](http://mackerell.umaryland.edu/charmm_drude_ff.shtml), and prepared a Drude .rtp file for a PEG 9-mer molecule. I obtained the partial charges and the atomic polarizabilities of the core and Drude particles using the prediction tool found at [MacKerell Lab](http://mackerell.umaryland.edu/software.shtml).

I have then generated a system which consists of 185 PEG 9-mers and 315 SWM4-NDP water molecules, and applied energy minimization, nvt and npt equilibration steps at 273K. The equilibration was successful. However, I found out that temperatures did not equilibrate at exactly 273K, but around 270K. The deviation in temperature became larger when I raised the system temperature to a higher value, e.g., 378K, and the temperature ended up equilibrating at 370K. I used a timestep of 1fs, and the temperature deviation was larger when a timestep of 2fs was used. I have checked the density, pressure, and the configuration, they all looked ok except that the temperature was a bit lower than the thermostat temperature.

This is the .mdp file I am using for npt equilibration. I have tried changing the tau\_t value, but the deviation in temperature still existed.  
integrator = md  
dt = 0.001  
nsteps = 5000000  
comm-grps = SYSTEM  
comm-mode = Linear  
energygrps =  
;  
nstxout = 0  
nstvout = 0  
nstfout = 0  
nstlog = 500  
nstenergy = 500  
nstcalcenergy =1  
nstxout-compressed = 2000  
compressed-x-grps = system  
;  
annealing = single  
annealing\_npoints = 2  
annealing\_time = 0 50 ;ps  
annealing\_temp = 0 273 ;K  
;  
pbc = xyz  
cutoff-scheme = Verlet  
coulombtype = PME  
rcoulomb = 1.2  
vdwtype = cut-off  
rvdw = 1.2  
DispCorr = EnerPres  
;  
Tcoupl = V-rescale  
tau\_t = 0.1  
tc\_grps = system  
ref\_t = 273  
;  
Pcoupl = Berendsen  
pcoupltype = isotropic  
tau\_p = 0.5  
ref\_p = 1.0  
refcoord-scaling = all  
compressibility = 4.5e-5  
;  
gen\_vel = no  
gen\_temp = 298.15  
gen\_seed = -1  
;  
freezegrps =  
freezedim =  
constraints = h-bonds

; DRUDE PARAMETERS  
drude = yes  
drude-mode = SCF  
drude-hyper = yes  
drude-khyp = 16736000.0  
drude-r = 0.02  
drude-pow = 4

I was wondering if anyone has experience with this problem. Any help would be greatly appreciated. Thanks in advance for your time!