[gmx-users] DPOSRES not working

[Sergio Manzetti]

Hi Johannes, yes, they are there in both cases: 

; Include Position restraint file 
#ifdef POSRES 
#include "posre_DNA_chain_E.itp" 
#endif 



Sergio Manzetti 

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

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
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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 11:29:03 AM 
Subject: Re: [gmx-users] DPOSRES not working 

Okay, but what did you define in your topologies for your DNA chains: 

#include "topol_DNA_chain_E.itp" 
#include "topol_DNA_chain_F.itp" 

Make sure that at the end of these files you have lines stating e.g: 

; Include Position restraint file 
#ifdef POSRES 
#include "posre_DNA_chain_E.itp" 
#endif 

The same for your other chain. 

Normally pdb2gmx creats a position restrain file posre_DNA_chain_E.itp 
for all the heavy atoms. If you do not have this position restrain file 
you can generate it with gmx genrestr. 

Last but not least you can read about position restrains in the manual. 

All the best 
Johannes 


On 07.09.2017 11:15, Sergio Manzetti wrote: 
> 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 
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] 
> 
> 
> 
> 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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