[gmx-users] FW: Position Restraints problem
Chiara Bello
kiarabell at msn.com
Thu Oct 15 14:47:32 CEST 2015
Thank you very much, I'll take your advice!
> To: gmx-users at gromacs.org
> From: jalemkul at vt.edu
> Date: Thu, 15 Oct 2015 07:44:29 -0400
> Subject: Re: [gmx-users] FW: Position Restraints problem
>
>
>
> On 10/15/15 5:28 AM, Chiara Bello wrote:
> >
> >
> >
> >
> >
> > From: kiarabell at msn.com
> > To: gmx-users at gromacs.org
> > Subject: RE: [gmx-users] Position Restraints problem
> > Date: Thu, 15 Oct 2015 09:20:49 +0000
> >
> >
> >
> >
> > I'm sorry but I don't think my case is one of the phenomena described in the list, the problem appears after applying the restraints, and not after the pbc. Using explicit solvent method I didn't detect this problem, using the method of implicit solvent instead the structure appears as attached.
> > This is the mdp file I used to apply the restraints:
> >
> > ; run parameters for position restraints
> > ; with temperature and pressure equilibration
> > ; values appropriate for CHARMM27 force field
> >
> > include = -I. -I.. -I../top
> > define = -DPOSRES
> >
> > integrator = md
> > tinit = 0.0
> > dt = 0.002
> > nsteps = 12500
> >
> > nstxout = 500
> > nstvout = 500
> > nstfout = 500
> >
> > nstlog = 500
> > nstenergy = 500
> >
> > comm-mode = Linear
> > nstcomm = 1000
> > comm-grps = SYSTEM
> >
> > nstlist = 5
> > ns_type = grid
> > pbc = xyz
> > rlist = 1.0
> >
> > coulombtype = Cut-off
> > rcoulomb = 1.2
> > epsilon_r = 1
> > epsilon_rf = 54
> >
> > vdw-type = Cut-off
> > rvdw-switch = 1.0
> > rvdw = 1.2
> >
> > DispCorr = EnerPres
> > fourierspacing = 0.12
> >
> > pme_order = 4
> > ewald_rtol = 1e-05
> > ewald_geometry = 3d
> > epsilon_surface = 0
> > optimize_fft = yes
> >
> > Tcoupl = V-rescale
> > tau_t = 0.1
> > tc-grps = protein
> > ref_t = 300
> >
> > Pcoupl = berendsen
> > Pcoupltype = isotropic
> >
> > tau_p = 0.5
> > compressibility = 4.5e-5
> > ref_p = 1.0
> > refcoord_scaling = COM
> >
> > gen_vel = yes
> > gen-temp = 300
> > gen_seed = -1
> >
> > constraints = all-bonds
> > constraint-algorithm = Lincs
> > lincs-order = 4
> > lincs-iter = 1
> >
> > ; Implicit solvent
> > implicit_solvent = GBSA
> > gb_algorithm = OBC
> > nstgbradii = 1.0
> > rgbradii = 1.0
> > gb_epsilon_solvent = 80
> > gb_dielectric_offset = 0.009
> > sa_algorithm = Ace-approximation
> > sa_surface_tension = 0.0054
> >
>
> Setting up a periodic system with pressure coupling, while using an implicit
> solvent, does not make sense. This explains the "breaking" of your system,
> because the box compresses down to the size of the protein, meaning all frames
> will cross PBC and appear broken. Implicit systems should be set up without
> PBC, no pressure coupling, and longer cutoffs.
>
> -Justin
>
> >
> > My itp file:
> >
> >
> >
> > ; i funct fcx fcy fcz
> > 175 1 1000 1000 1000
> > 176 1 1000 1000 1000
> > 177 1 1000 1000 1000
> > 178 1 1000 1000 1000
> > 179 1 1000 1000 1000
> > 180 1 1000 1000 1000
> > 181 1 1000 1000 1000
> > 182 1 1000 1000 1000
> > 183 1 1000 1000 1000
> > 184 1 1000 1000 1000
> > 185 1 1000 1000 1000
> > 186 1 1000 1000 1000
> > 187 1 1000 1000 1000
> > 188 1 1000 1000 1000
> > 189 1 1000 1000 1000
> > 190 1 1000 1000 1000
> > 191 1 1000 1000 1000
> > 192 1 1000 1000 1000
> > 193 1 1000 1000 1000
> > 194 1 1000 1000 1000
> > 195 1 1000 1000 1000
> > 196 1 1000 1000 1000
> > 197 1 1000 1000 1000
> > 198 1 1000 1000 1000
> > 199 1 1000 1000 1000
> > 200 1 1000 1000 1000
> > 201 1 1000 1000 1000
> > 202 1 1000 1000 1000
> > 203 1 1000 1000 1000
> > 204 1 1000 1000 1000
> > 205 1 1000 1000 1000
> > 206 1 1000 1000 1000
> > 207 1 1000 1000 1000
> > 208 1 1000 1000 1000
> > 209 1 1000 1000 1000
> > 210 1 1000 1000 1000
> > 211 1 1000 1000 1000
> > 212 1 1000 1000 1000
> > 213 1 1000 1000 1000
> > 214 1 1000 1000 1000
> > 215 1 1000 1000 1000
> > .....etc
> >
> > My top file;
> >
> > Command line was:
> > ; pdb2gmx -f 4AKE.pdb -o protein.pdb -p 4ake.top -i protein_posre.itp -ff charmm27 -nochargegrp
> > ;
> > ; Force field was read from the standard Gromacs share directory.
> > ;
> >
> > ; Include forcefield parameters
> > #include "charmm27.ff/forcefield.itp"
> >
> > [ moleculetype ]
> > ; Name nrexcl
> > Protein_chain_A 3
> >
> > [ atoms ]
> > ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
> > ; residue 1 MET rtp MET q +1.0
> > 1 NH3 1 MET N 1 -0.3 14.007 ; qtot -0.3
> > 2 HC 1 MET H1 2 0.33 1.008 ; qtot 0.03
> > 3 HC 1 MET H2 3 0.33 1.008 ; qtot 0.36
> > ....etc
> >
> > Include Position restraint file
> > #ifdef POSRES
> > #include "helices.itp"
> > #endif
> >
> > [ system ]
> > ; Name
> > ADENYLATE KINASE
> >
> > [ molecules ]
> > ; Compound #mols
> > Protein_chain_A 1
> >
> >
> >
>
> --
> ==================================================
>
> 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
>
> ==================================================
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