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
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From: "Hermann, Johannes" <j.herm...@lrz.tu-muenchen.de>
To: "gmx-users" <gmx-us...@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.herm...@lrz.tum.de
http://www.biovt.mw.tum.de/
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