[gmx-users] FW: Position Restraints problem
Justin Lemkul
jalemkul at vt.edu
Thu Oct 15 13:44:40 CEST 2015
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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