[gmx-users] DPOSRES not working

[Sergio Manzetti]

Hi Johannes, it appears so: 


; Include forcefield parameters 
#include "amber99sb-ildn.ff/forcefield.itp" 

; Include chain topologies 
#include "topol_DNA_chain_E.itp" 
#include "topol_DNA_chain_F.itp" 
#include "PRB_GMX.itp" 

; Include water topology 
#include "amber99sb-ildn.ff/spc.itp" 

#ifdef POSRES_WATER 
; Position restraint for each water oxygen 
[ position_restraints ] 
; i funct fcx fcy fcz 
1 1 1000 1000 1000 
#endif 

; Include topology for ions 
#include "amber99sb-ildn.ff/ions.itp" 

[ system ] 
; Name 
CRYSTAL STRUCTURE OF P53 CORE DOMAIN IN COMPLEX WITH DNA in water 

[ molecules ] 
; Compound #mols 
DNA_chain_E 1 
DNA_chain_F 1 
NA 71 
CL 31 
PRB 1 
SOL 16349 



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 
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From: "Hermann, Johannes" <J.Hermann at lrz.tu-muenchen.de> 
To: "gmx-users" <gmx-users at gromacs.org> 
Sent: Thursday, September 7, 2017 11:18:29 AM 
Subject: Re: [gmx-users] DPOSRES not working 

Dear Sergio, 

how did you define the position restrain in your topology? Check your 
topology and position restrain file. 

All the best 

Johannes 


On 07.09.2017 11:07, Sergio Manzetti wrote: 
> Hello, I am running 5 simulations with the given mdp: 
> 
> title = DNA in water stabilization 
> cpp = /lib/cpp 
> include = -I../top 
> define = -DPOSRES 
> integrator = md 
> dt = 0.002 
> nsteps = 10000000 
> nstxout = 5000 
> nstvout = 5000 
> nstlog = 5000 
> nstenergy = 300 
> nstxout-compressed = 300 
> compressed-x-grps = PRB SOL NA CL DNA 
> energygrps = PRB SOL NA CL DNA 
> nstlist = 10 
> ns-type = grid 
> rlist = 0.8 
> coulombtype = PME 
> rcoulomb = 0.8 
> rvdw = 0.8 
> tcoupl = V-Rescale 
> tc-grps = System 
> tau-t = 0.1 
> ref-t = 310 
> Pcoupl = No 
> tau-p = 1.0 
> compressibility = 4.5e-5 
> ref-p = 1.0 
> gen-vel = yes 
> gen-temp = 310 
> gen-seed = 17527 
> constraints = all-bonds 
> 
> 
> and still, the DNA splits into two.... 
> 
> Any ideas what could be wrong? 
> 
> 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 ] 
> 

-- 
______________________________________ 
*Technische Universität München* 
*Johannes Hermann, M.Sc.* 
Lehrstuhl für Bioverfahrenstechnik 
Boltzmannstr. 15 
D-85748 Garching 
Tel: +49 8928915730 
Fax: +49 8928915714 

Email: j.hermann at lrz.tum.de 
http://www.biovt.mw.tum.de/ 

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