Hi, I have a question about refcoord_scaling option and its role in pressure coupling. What I'm currently doing is just running the lysozyme tutorial on my own protein. I've so far had successful runs when equilibrating on my own machine, which is currently running gmx4.5.3. NPT came to a stable average of ~1.0 bar. But when I do it on the cluster with gmx4.5.5, grompp gives the following error:
WARNING 1 [file npt.mdp]: You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option. My npt.mdp file is as follows (straight from the tutorial at this stage): define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 150000 ; 2 * 150000 = 300 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = yes ; Restarting after NVT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off The only change I made is the nsteps as my box is bigger and thus has more waters in it. So after reading the warning I tried to find some info on the refcoord_scaling, which the only information found by my feeble attempts were from the mdp options and the manual, which states: *refcoord_scaling:* *no*The reference coordinates for position restraints are not modified. Note that with this option the virial and pressure will depend on the absolute positions of the reference coordinates.*all*The reference coordinates are scaled with the scaling matrix of the pressure coupling.*com*Scale the center of mass of the reference coordinates with the scaling matrix of the pressure coupling. The vectors of each reference coordinate to the center of mass are not scaled. Only one COM is used, even when there are multiple molecules with position restraints. For calculating the COM of the reference coordinates in the starting configuration, periodic boundary conditions are not taken into account. I don't quite understand this completely, is the option there to change the coordinates of the solute as the box size changes, where the 'all' option changes the coordinates of every atom and the com only changes the coordinates of the solute com? Please correct me on this. So before posting this question I ran a few npt equilibrations with the all and com options chosen with parrinello-rahman from 100 ps, to 300 ps, and to 1000 ps. All with 10 different initial velocities from the nvt. The reason for increasing time is that the equilibration did not reach the target 1 bar and ended at averages of 4-7 bars for the 10 equilibrations. The oscillation was comparable to the graph seen on the lysozyme tutorial between 0-400. So I tried running berendsen instead of parrinello rahman as the manual says it should help me get to the target pressure better and I can follow up with parrinello-rahman. But the pressure still didn't reach the target pressure. So the questions are, - is my naive understanding of the refcoord_scaling correct? if not will you help explain it to me or point me to a link that could help me? - Also, when pressure oscillations are at 100s of bars, is 3-6 bar difference from 1 bar going to make any difference? (it should. shouldn't it?) - Or have I made some other careless mistake? If you need more information, I'd be happy to provide them.
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