[gmx-users] MDP for DNA with ions

[Sergio Manzetti]

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 
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 
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 

Sergio 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory  ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Justin Lemkul" <jalemkul at vt.edu> 
To: "gmx-users" <gmx-users at gromacs.org> 
Sent: Thursday, June 22, 2017 3:07:03 PM 
Subject: Re: [gmx-users] MDP for DNA with ions 

On 6/22/17 8:56 AM, Sergio Manzetti wrote: 
> HI, I use mdp for simulating with a 2fs time step, nstlist 10, rlist 1.2, rcoulomb 1.2, rvdw 1.2, V-rescale, no P-coupling. Lincs on all bonds, still the DNA system won't minimize . 
> 
> What is your experience with DNA simulations and these settings? Do you have an mdp file that may be generally good for DNA sims? 
> 

Settings depend on the force field, not the molecules in the system. If you 
want commentary, please provide a full .mdp file, not just select settings. 

-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 

================================================== 
-- 
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 http://www.gromacs.org/Support/Mailing_Lists 

* For (un)subscribe requests visit 
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.