[gmx-users] MDP for DNA with ions

[Sergio Manzetti]

OK, thanks for this! 


Sergio Manzetti 

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From: "Justin Lemkul" <jalemkul at vt.edu> 
To: "gmx-users" <gmx-users at gromacs.org> 
Sent: Thursday, June 22, 2017 3:17:02 PM 
Subject: Re: [gmx-users] MDP for DNA with ions 

On 6/22/17 9:09 AM, Sergio Manzetti wrote: 
> I use the AMBER99SB-ILDN ff for a piece of DNA taken from the RCSB database. Removed all waters and non-nucleic acid molecules, and everything seems fine. 
> 
> The mdp settings are: 
> 
> title = DNA in water stabilization 
> cpp = /lib/cpp 
> include = -I../top 
> define = 
> integrator = md 
> dt = 0.002 
> nsteps = 5000000 
> nstxout = 5000 
> nstvout = 5000 
> nstlog = 5000 
> nstenergy = 300 
> nstxout-compressed = 300 
> compressed-x-grps = DNA SOL NA CL 
> energygrps = DNA SOL NA CL 
> nstlist = 10 
> ns-type = grid 
> rlist = 1.2 
> coulombtype = PME 
> rcoulomb = 1.2 
> rvdw = 1.2 

AMBER uses shorter cutoffs. Refer to their papers for what is correct. 

> tcoupl = V-Rescale 
> tc-grps = DNA SOL NA CL 
> tau-t = 0.1 0.1 0.1 0.1 
> ref-t = 310 310 310 310 

Don't do this. 

http://www.gromacs.org/Documentation/Terminology/Thermostats#What_No_To_Do 

> Pcoupl = No 
> tau-p = 1.0 
> compressibility = 4.5e-5 
> ref-p = 1.0 
> gen-vel = yes 
> gen-temp = 310 
> gen-seed = 173529 
> constraints = all-bonds 

IIRC AMBER only constrains bonds to H, so again check the literature. 

None of these points is likely fatal (maybe the thermostat) but you should use 
correct settings. If your system is crashing with this .mdp file or the 
corrected one, it's because you haven't adequately minimized and equilibrated. 

-Justin 

-- 
================================================== 

Justin A. Lemkul, Ph.D. 
Ruth L. Kirschstein NRSA Postdoctoral Fellow 

Department of Pharmaceutical Sciences 
School of Pharmacy 
Health Sciences Facility II, Room 629 
University of Maryland, Baltimore 
20 Penn St. 
Baltimore, MD 21201 

jalemkul at outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul 

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