<HTML><BODY><DIV style='font-family: "Verdana"; font-size: 10pt;'><DIV>
<DIV>Thanks David,</DIV>
<DIV> </DIV>
<DIV>Now everything seems to work. But why with order 6 was working in 3.2.1 and not now? can you give me a reference where I can learn more about what all pme parameter mean? and how to set up them?.</DIV>
<DIV> </DIV>
<DIV>Thank you, Hector</DIV> <BR>-----Original Message-----<BR>From: David <spoel@xray.bmc.uu.se><BR>To: Discussion list for GROMACS users <gmx-users@gromacs.org><BR>Sent: Fri, 11 Nov 2005 20:21:50 +0100<BR>Subject: Re: [gmx-users] pme problems in gromacs 3.3<BR><BR>
<STYLE>
.AOLPlainTextBody {
margin: 0px;
font-family: Tahoma, Verdana, Arial, Sans-Serif;
font-size: 12px;
color: #000;
background-color: #fff;
}
.AOLPlainTextBody pre {
font-size: 9pt;
}
.AOLInlineAttachment {
margin: 10px;
}
.AOLAttachmentHeader {
border-bottom: 2px solid #E9EAEB;
background: #F9F9F9;
}
.AOLAttachmentHeader .Title {
font: 11px Tahoma;
font-weight: bold;
color: #666666;
background: #E9EAEB;
padding: 3px 0px 1px 10px;
}
.AOLAttachmentHeader .FieldLabel {
font: 11px Tahoma;
font-weight: bold;
color: #666666;
padding: 1px 10px 1px 9px;
}
.AOLAttachmentHeader .FieldValue {
font: 11px Tahoma;
color: #333333;
}
</STYLE>
<DIV class=AOLPlainTextBody id=AOLMsgPart_0_110dda1c-1acd-4720-8132-070976e551e5><PRE><TT>On Fri, 2005-11-11 at 14:07 -0500, <A href="mailto:hseara%40netscape.net">hseara@netscape.net</A> wrote:
> Dear everyone,
>
> I'm trying to perform a bilayer simulation with the new gromacs 3.3
> that works fine with the older version 3.2.1. The problem as far as I
> know is related to something around "pme". When I turn it off and use
> cut-off every think works fine. Here is my dun.mdp file when I turn pme
> on in gromacs 3.3. The same system in gromacs 3.2.1 with this pme file
> works perfectly. Any help will be apreciated.
try pme_order = 4
>
> ;
> ; File 'mdout.mdp' was generated
> ; By user: hector (500)
> ; On host: hectorp
> ; At date: Tue Nov 8 22:26:19 2005
> ;
>
> ; VARIOUS PREPROCESSING OPTIONS
> title = MD run on DOPS
> ; Preprocessor - specify a full path if necessary.
> cpp = /usr/bin/cpp
> include =
> define =
>
> ; RUN CONTROL PARAMETERS
> integrator = md
> ; Start time and timestep in ps
> tinit = 0
> dt = 0.001
> nsteps = 20000
> ; For exact run continuation or redoing part of a run
> init_step = 0
> ; mode for center of mass motion removal
> comm-mode = Linear
> ; number of steps for center of mass motion removal
> nstcomm = 1
> ; group(s) for center of mass motion removal
> comm-grps =
>
> ; LANGEVIN DYNAMICS OPTIONS
> ; Friction coefficient (amu/ps) and random seed
> bd-fric = 0
> ld-seed = 1993
>
> ; ENERGY MINIMIZATION OPTIONS
> ; Force tolerance and initial step-size
> emtol = 50
> emstep = 0.05
> ; Max number of iterations in relax_shells
> niter = 0
> ; Step size (ps^2) for minimization of flexible constraints
> fcstep = 0
> ; Frequency of steepest descents steps when doing CG
> nstcgsteep = 15000
> nbfgscorr = 10
>
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout = 500
> nstvout = 500
> nstfout = 0
> ; Checkpointing helps you continue after crashes
> nstcheckpoint = 1000
> ; Output frequency for energies to log file and energy file
> nstlog = 500
> nstenergy = 500
> ; Output frequency and precision for xtc file
> nstxtcout = 0
> xtc-precision = 1000
> ; This selects the subset of atoms for the xtc file. You can
> ; select multiple groups. By default all atoms will be written.
> xtc-grps =
> ; Selection of energy groups
> energygrps =
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist = 3
> ; ns algorithm (simple or grid)
> ns_type = grid
> ; Periodic boundary conditions: xyz (default), no (vacuum)
> ; or full (infinite systems only)
> pbc = xyz
> ; nblist cut-off
> rlist = 0.95
> domain-decomposition = no
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype = pme
> rcoulomb-switch = 0
> rcoulomb = 0.95
> ; Relative dielectric constant for the medium and the reaction field
> epsilon-r = 1
> epsilon_rf = 1
> ; Method for doing Van der Waals
> vdw-type = Cut-off
> ; cut-off lengths
> rvdw-switch = 0
> rvdw = 1.8
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = EnerPres
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension = 1
> ; Seperate tables between energy group pairs
> energygrp_table =
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing = 0.12
> ; FFT grid size, when a value is 0 fourierspacing will be used
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> ; EWALD/PME/PPPM parameters
> pme_order = 6
> ewald_rtol = 1e-05
> ewald_geometry = 3d
> epsilon_surface = 0
> optimize_fft = no
>
> ; GENERALIZED BORN ELECTROSTATICS
> ; Algorithm for calculating Born radii
> gb_algorithm = Still
> ; Frequency of calculating the Born radii inside rlist
> nstgbradii = 1
> ; Cutoff for Born radii calculation; the contribution from atoms
> ; between rlist and rgbradii is updated every nstlist steps
> rgbradii = 2
> ; Salt concentration in M for Generalized Born models
> gb_saltconc = 0
>
> ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
> implicit_solvent = No
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> Tcoupl = nose-hoover
> ; Groups to couple separately
> tc-grps = DOPS DOPA SOL NA+
> ; Time constant (ps) and reference temperature (K)
> tau-t = 0.2 0.2 0.2 0.2
> ref-t = 303.0 303.0 303.0 303.0
> ; Pressure coupling
> Pcoupl = Parrinello-Rahman
> Pcoupltype = semiisotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau_p = 1.0 1.0
> compressibility = 4.5e-5 4.5e-5
> ref_p = 1.01325 1.01325
> ; Random seed for Andersen thermostat
> andersen_seed = 815131
>
> ; OPTIONS FOR QMMM calculations
> QMMM = no
> ; Groups treated Quantum Mechanically
> QMMM-grps =
> ; QM method
> QMmethod =
> ; QMMM scheme
> QMMMscheme = normal
> ; QM basisset
> QMbasis =
> ; QM charge
> QMcharge =
> ; QM multiplicity
> QMmult =
> ; Surface Hopping
> SH =
> ; CAS space options
> CASorbitals =
> CASelectrons =
> SAon =
> SAoff =
> SAsteps =
> ; Scale factor for MM charges
> MMChargeScaleFactor = 1
> ; Optimization of QM subsystem
> bOPT =
> bTS =
>
> ; SIMULATED ANNEALING
> ; Type of annealing for each temperature group (no/single/periodic)
> annealing = no
> ; Number of time points to use for specifying annealing in each group
> annealing_npoints =
> ; List of times at the annealing points for each group
> annealing_time =
> ; Temp. at each annealing point, for each group.
> annealing_temp =
>
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel = no
> gen-temp = 300
> gen-seed = 533671
>
> ; OPTIONS FOR BONDS
> constraints = all-bonds
> ; Type of constraint algorithm
> constraint-algorithm = LINCS
> ; Do not constrain the start configuration
> unconstrained-start = yes
> ; Use successive overrelaxation to reduce the number of shake iterations
> Shake-SOR = no
> ; Relative tolerance of shake
> shake-tol = 0.0001
> ; Highest order in the expansion of the constraint coupling matrix
> lincs-order = 4
> ; Number of iterations in the final step of LINCS. 1 is fine for
> ; normal simulations, but use 2 to conserve energy in NVE runs.
> ; For energy minimization with constraints it should be 4 to 8.
> lincs-iter = 1
> ; Lincs will write a warning to the stderr if in one step a bond
> ; rotates over more degrees than
> lincs-warnangle = 90
> ; Convert harmonic bonds to morse potentials
> morse = no
>
> ; ENERGY GROUP EXCLUSIONS
> ; Pairs of energy groups for which all non-bonded interactions are
> excluded
> energygrp_excl =
>
> ; NMR refinement stuff
> ; Distance restraints type: No, Simple or Ensemble
> disre = No
> ; Force weighting of pairs in one distance restraint: Conservative or
> Equal
> disre-weighting = Conservative
> ; Use sqrt of the time averaged times the instantaneous violation
> disre-mixed = no
> disre-fc = 1000
> disre-tau = 0
> ; Output frequency for pair distances to energy file
> nstdisreout = 100
> ; Orientation restraints: No or Yes
> orire = no
> ; Orientation restraints force constant and tau for time averaging
> orire-fc = 0
> orire-tau = 0
> orire-fitgrp =
> ; Output frequency for trace(SD) and S to energy file
> nstorireout = 100
> ; Dihedral angle restraints: No, Simple or Ensemble
> dihre = No
> dihre-fc = 1000
> dihre-tau = 0
> ; Output frequency for dihedral values to energy file
> nstdihreout = 100
>
> ; Free energy control stuff
> free-energy = no
> init-lambda = 0
> delta-lambda = 0
> sc-alpha = 0
> sc-power = 1
> sc-sigma = 0.3
>
> ; Non-equilibrium MD stuff
> acc-grps =
> accelerate =
> freezegrps =
> freezedim =
> cos-acceleration = 0
> deform =
>
> ; Electric fields
> ; Format is number of terms (int) and for all terms an amplitude (real)
> ; and a phase angle (real)
> E-x =
> E-xt =
> E-y =
> E-yt =
> E-z =
> E-zt =
>
> ; User defined thingies
> user1-grps =
> user2-grps =
> userint1 = 0
> userint2 = 0
> userint3 = 0
> userint4 = 0
> userreal1 = 0
> userreal2 = 0
> userreal3 = 0
> userreal4 = 0
> ___________________________________________________
> Try the New Netscape Mail Today!
> Virtually Spam-Free | More Storage | Import Your Contact List
> <A href="http://mail.netscape.com" target=_blank>http://mail.netscape.com</A>
>
> _______________________________________________
> gmx-users mailing list
> <A href="mailto:gmx-users%40gromacs.org">gmx-users@gromacs.org</A>
> <A href="http://www.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://www.gromacs.org/mailman/listinfo/gmx-users</A>
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to <A href="mailto:gmx-users-request%40gromacs.org">gmx-users-request@gromacs.org</A>.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
<A href="mailto:spoel%40xray.bmc.uu.se">spoel@xray.bmc.uu.se</A> <A href="mailto:spoel%40gromacs.org">spoel@gromacs.org</A> <A href="http://xray.bmc.uu.se/~spoel" target=_blank>http://xray.bmc.uu.se/~spoel</A>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list
<A href="mailto:gmx-users%40gromacs.org">gmx-users@gromacs.org</A>
<A href="http://www.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://www.gromacs.org/mailman/listinfo/gmx-users</A>
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to <A href="mailto:gmx-users-request%40gromacs.org">gmx-users-request@gromacs.org</A>.
</TT></PRE></DIV><!-- end of AOLMsgPart_0_110dda1c-1acd-4720-8132-070976e551e5 --></DIV></DIV>
<hr style="MARGIN-TOP:10px" >
<b>Try the New Netscape Mail Today!</b><br />
Virtually Spam-Free | More Storage | Import Your Contact List<br /><a href="http://mail.netscape.com">http://mail.netscape.com</a>
</BODY></HTML>