[gmx-users] structure changed after energy minimization
Smith, Micholas D.
smithmd at ornl.gov
Tue Sep 1 14:21:24 CEST 2015
An additional measure that may help is to use either STRIDE or DSSP on the intial and final structures and try to quantify how much the secondary structure has really changed.
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Tuesday, September 01, 2015 8:16 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] structure changed after energy minimization
On 9/1/15 8:14 AM, Smith, Micholas D. wrote:
> Hi Sana Saeed,
> What force field are you using? Also are you sure the structure you are starting with is stable to begin with? It is possible that the model you are starting with is actually fairly far away from the minimum energy structure in which case energy minimization may alter the structure (though i've never seen a beta sheet changing into a coil-like form).
Worth noting that visualization software sometimes fails to render secondary
structure correctly. Analyzing the hydrogen bonding and backbone dihedrals is
definitive; whatever VMD/PyMOL/etc come up with is not.
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Sana Saeed <bioinformatic.lady at yahoo.com>
> Sent: Monday, August 31, 2015 10:30 PM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] structure changed after energy minimization
> hi gmx users,i want to simulate prion protein(beta-sheets structure; model in modeller), but after minimization the structure totally changes into elongated form.what am i missing? i am doing implicit solvent simulation. this is the mdp file for minimization: title =cpp = /lib/cpp ; prepocessor of the current machinedefine = -DFLEXIBLE ; -DPOSRES, -DPOSRES_IONS ;DFLEX_SPC; FLEXible SPC and POSition REStraints
> integrator = steep ; steepest descent algorithmdt = 0.005 ; time step in psnsteps = 5000 ; number of steps
> emtol = 100 ; convergence criterionemstep = 0.05 ; intial step sizeconstraints = noneconstraint-algorithm = lincsunconstrained-start = no ; Do not constrain the start configuration;shake_tol = 0.0001nstlist = 1 ; step frequency for updating neighbour listns_type = simple ; grid ; method for nighbour searching (?)nstxout = 100 ; frequency for writing coords to outputnstvout = 100 ; frequency for writing velocities to outputnstfout = 0 ; frequency for writing forces to outputnstlog =
> 100 ; frequency for writing energies to log filenstenergy = 100 ; frequency for writing energies to energy filenstxtcout = 0 ; frequency for writing coords to xtc trajxtc_grps = system ; group(s) whose coords are to be written in xtc trajenergygrps = system ; group(s) whose energy is to be written in energy filepbc = xyz ; use pbcrlist = 1.0 ; cutoff (nm)coulombtype = cutoff ; truncation for minimisation, with large cutoffrcoulomb = 1.0vdwtype = cut-off ; truncation for minimisation, with large cutoffrvdw = 1.0nstcomm = 0 ; number of steps for centre of mass motion removal (in vacuo only!)Tcoupl = noPcoupl = nogen_vel = no Free energy control stufffree_energy = yesinit_lambda = 0.0delta_lambda = 0sc_alpha =0.5sc-power
> =1.0sc-sigma = 0.3
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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
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