Hello Dr.Spoel and others,<br>There is one more problem with the simulation of hen egg white lysozyme simulation in water I am running. The timestep I could use is just 0.5 fs or 0.0005ps. Is there any way around to increase the timestep.
<br>This is how a part of my mdp file looks like:<br><br>; RUN CONTROL PARAMETERS = <br>integrator = md<br>;emstep = 0.001<br>;emtol = 100<br>; start time and timestep in ps =
<br>tinit = 0.0<br>dt = 0.0005<br>nsteps = 2000000<br>; number of steps for center of mass motion removal = <br>comm_mode = Angular <br>nstcomm = 1
<br>comm_grps = Protein_A <br><br>; This selects the subset of atoms for the xtc file. You can = <br>; select multiple groups. By default all atoms will be written. = <br>xtc-grps = <br>; Selection of energy groups =
<br>energygrps = Protein_A SOL Na Cl<br><br>; OPTIONS FOR WEAK COUPLING ALGORITHMS = <br>; Temperature coupling = <br>tcoupl = Berendsen<br>; Groups to couple separately = <br>tc-grps = Protein_A SOL Na Cl
<br>; Time constant (ps) and reference temperature (K) = <br>tau_t = 0.1 0.1 0.1 0.1<br>ref_t = 328 328 328 328<br>; Pressure coupling = <br>Pcoupl = Berendsen
<br>Pcoupltype = isotropic<br>; Time constant (ps), compressibility (1/bar) and reference P (bar) = <br>tau_p = 1.0 <br>compressibility = 5e-5<br>ref_p = 1.0
<br><br>; SIMULATED ANNEALING CONTROL = <br>annealing = no no no no<br>; Time at which temperature should be zero (ps) = <br>;zero_temp_time = 0<br><br>; GENERATE VELOCITIES FOR STARTUP RUN = <br>
gen_vel = yes<br>gen_temp = 328<br>gen_seed = 473529<br><br>; OPTIONS FOR BONDS = <br>constraints = none<br>; Type of constraint algorithm = <br>constraint_algorithm = SHAKE
<br>; Do not constrain the start configuration = <br>unconstrained_start = no<br>; Relative tolerance of shake = <br>shake_tol = 0.00001<br>; Highest order in the expansion of the constraint coupling matrix =
<br>lincs_order = 4<br>; Lincs will write a warning to the stderr if in one step a bond = <br>; rotates over more degrees than = <br>lincs_warnangle = 30<br>; Convert harmonic bonds to morse potentials =
<br>morse = no<br><br>; NMR refinement stuff = <br>; Distance restraints type: No, Simple or Ensemble = <br>disre = No<br>; Force weighting of pairs in one distance restraint: Equal or Conservative =
<br>disre_weighting = Equal<br>; Use sqrt of the time averaged times the instantaneous violation = <br>disre_mixed = no<br>disre_fc = 1000<br>disre_tau = 1.25<br>; Output frequency for pair distances to energy file =
<br>nstdisreout = 100<br><br>; Free energy control stuff = <br>free_energy = no<br>init_lambda = 0<br>delta_lambda = 0<br>sc-alpha = 0<br>sc-sigma =
0.3<br><br>Thanks,<br>-Vissu.<br><br><div><span class="gmail_quote">On 8/11/06, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Viswanadham Sridhara wrote:<br>> Hello everyone,<br>> I could figure out that parameters for NAG are not that important. So, I<br>> used free HEWL.<br>> I started running it, but I realize that the protein started to rotate
<br>> around the center of mass with a frequency of around 200ps.<br>> I used "Linear" as an option for comm_mode and I used "Protein" in<br>> comm_grps.<br>> Any reason Why the protein is rotating around its center of mass, is it
<br>> normal?<br><br>yes.<br><br>comm_mode = angular<br><br>> Thanks in advance.<br>> -Vissu.<br>><br>> ---------- Forwarded message ----------<br>> From: *David Mobley* <<a href="mailto:dmobley@gmail.com">
dmobley@gmail.com</a> <mailto:<a href="mailto:dmobley@gmail.com">dmobley@gmail.com</a>>><br>> Date: Aug 8, 2006 12:32 AM<br>> Subject: Re: [gmx-users] Hen egg white lysozyme.<br>> To: Discussion list for GROMACS users <
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>><br>><br>> Vissu,<br>><br>> Depends on what you are trying to do. Many proteins deposited in the
<br>> pdb contain "uninteresting" ligands bound to them (i.e. cosolvent<br>> molecules, etc.) On the other hand, sometimes ligands are functionally<br>> important or significantly affect the structure. You have to decide
<br>> whether you want to include NAG or not; it might help to first figure<br>> out what it is and what it's used for (perhaps look up its name, and<br>> look at the paper and PDB headers...).<br>><br>> It is obviously harder to come up with parameters for NAG than not. If
<br>> you end up deciding it's not important, you can, for example, just<br>> remove the HETATM entries dealing with it before running pdb2gmx.<br>><br>> David<br>><br>><br>> On 8/7/06, Viswanadham Sridhara <
<a href="mailto:muta.mestri@gmail.com">muta.mestri@gmail.com</a><br>> <mailto:<a href="mailto:muta.mestri@gmail.com">muta.mestri@gmail.com</a>>> wrote:<br>> > Hi Everyone,<br>> > I am trying to simulate a protein and I am getting the following error
<br>> > message.<br>> > "NAG" not found in residue topology database. I checked gmx-users<br>> discussion<br>> > list to find out if someone ever used 1HEW.pdb . Its a hen egg-white<br>> > lysozyme. I did not get even a single archive about this.
<br>> > It is under HETATM section of .pdb file. Any help is appreciated.<br>> > I know that I have to add this residue in aminoacids.dat file and create<br>> > atoms and bonds in .rtp section. Is there any other way around?
<br>> > Thanks in advance,<br>> > -Vissu<br>> ><br>> > --<br>> > Viswanadham Sridhara,<br>> > Graduate Research Assistant,<br>> > Old Dominion University,<br>> > Norfolk, VA-23529.
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<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>><br>><br>> --<br>> Viswanadham Sridhara,<br>> Research Assistant,<br>
> Old Dominion University,<br>> Norfolk, Va-23529.<br>><br>><br>> ------------------------------------------------------------------------<br>><br>> _______________________________________________<br>
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http://www.gromacs.org/mailing_lists/users.php</a><br><br><br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se
</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>_______________________________________________
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</a><br></blockquote></div><br><br clear="all"><br>-- <br>Viswanadham Sridhara,<br>Research Assistant,<br>Old Dominion University,<br>Norfolk, Va-23529.