[gmx-users] DNA splitting in simulations

[Sergio Manzetti]

Jose, thanks for the DPOSRE. About the multiple tcoupling, as mentioned in the email, grompp wanted equal number of tcouplings as groups in the top file. 


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: "João Henriques" <joao.m.a.henriques at gmail.com> 
To: "gmx-users" <gmx-users at gromacs.org> 
Sent: Tuesday, June 27, 2017 11:51:17 AM 
Subject: Re: [gmx-users] DNA splitting in simulations 

Hi! 

Your mdp file doesn't tell the engine to apply the restraints during the 
simulation... You need to specify: 
define = -DPOSRES 

Also, didn't Justin already warn you about using separate temperature 
couplings for every component of your system? 

Please check the "What Not To Do" section under: 
http://www.gromacs.org/Documentation/Terminology/Thermostats 

Best regards, 
João 

On Tue, Jun 27, 2017 at 11:22 AM, Sergio Manzetti < 
sergio.manzetti at fjordforsk.no> wrote: 

> Hi, I Have run a DNA piece in a box of 7 7 7 , with NaCl ions 
> neutralizing, as discussed earlier. The simulation went fine without any 
> errors, however it turns out the DNA strands separate. The position 
> restraints made by pdb2gmx using the AMBERDB ISTN ff are not working ? 
> 
> This is the posres file: 
> In this topology include file, you will find position restraint 
> ; entries for all the heavy atoms in your original pdb file. 
> ; This means that all the protons which were added by pdb2gmx are 
> ; not restrained. 
> 
> [ position_restraints ] 
> ; atom type fx fy fz 
> 1 1 1000 1000 1000 
> 3 1 1000 1000 1000 
> 6 1 1000 1000 1000 
> 8 1 1000 1000 1000 
> 9 1 1000 1000 1000 
> 11 1 1000 1000 1000 
> 12 1 1000 1000 1000 
> 14 1 1000 1000 1000 
> 15 1 1000 1..................... 
> 
> 
> and here is the simulation mdp. 
> 
> 
> 
> 
> itle = 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 = 20 
> ns-type = grid 
> rlist = 0.8 
> coulombtype = PME 
> rcoulomb = 0.8 
> rvdw = 0.8 
> tcoupl = V-Rescale 
> tc-grps = SOL DNA NA CL 
> tau-t = 0.1 0.1 0.1 0.1 
> 
> 
> 
> Note that GMX gromp wanted 4 groups at tc_grps and tau_t, otherwise it 
> wouldn't proceed. 
> 
> 
> Thanks! 
> 
> 
> 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 ] 
> 
> -- 
> 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. 
-- 
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.