<div>Thank you all!</div>
<div> </div>
<div>How about -DFLEXIBLE in both em and md?</div>
<div> </div>
<div>Steven<br><br></div>
<div class="gmail_quote">On Tue, Feb 28, 2012 at 2:13 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div class="im"><br><br>lina wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">On Tue, Feb 28, 2012 at 10:07 PM, Steven Neumann <<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">Thank you Vedat!<br><br>Why do you use -DFLEXIBLE in md and in em?<br>Why dont you use constraint algorithm (LINCS) in your simulation?<br>
</blockquote><br>Otherwise, the system is easily explode with lots of LINCS warning.<br><br></blockquote><br></div>A system that is unstable will cause the LINCS algorithm to fail, but turning off constraints does not prevent a system from becoming unstable or crashing.<br>
<br>-Justin
<div>
<div class="h5"><br><br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">Also thanks Vedat for sharing,<br><br>Best regards,<br><br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">Steven<br><br>On Tue, Feb 28, 2012 at 12:14 PM, Vedat Durmaz <<a href="mailto:durmaz@zib.de" target="_blank">durmaz@zib.de</a>> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote"><br>hi steven,<br><br>i've been simulating a 33 AA peptide for the past two days using implicent<br>solvent in order to achieve a proper folding.<br>
<br>i haven't added counterions, however, the systems shows nice results<br>according to what i've expected. the mdrun command (for the extension) for<br>our hardware looks as follows:<br><br>mpiexec -np 4 mdrun -pd -s md.tpr -append -cpi md.cpt -deffnm md 2>&1<br>
<br>and here's the mdp file for the energy minimization:<br><br>define = -DFLEXIBLE<br>constraints = none<br>integrator = steep<br>dt = 0.001 ; ps<br>nsteps = 30000<br>
vdwtype = cut-off<br>coulombtype = cut-off<br>pbc = no<br>nstlist = 0<br>ns_type = simple<br>rlist = 0 ; this means all-vs-all (no cut-off), which<br>
gets expensive for bigger systems<br>rcoulomb = 0<br>rvdw = 0<br>comm-mode = angular<br>comm-grps = Protein<br>optimize_fft = yes<br>;<br>; Energy minimizing stuff<br>
;<br>emtol = 5.0<br>emstep = 0.01<br>;<br>; Implicit solvent<br>;<br>implicit_solvent = GBSA<br>gb_algorithm = Still ; HCT ; OBC<br>nstgbradii = 1<br>rgbradii = 0 ; [nm] Cut-off for the calculation of the Born<br>
radii. Currently must be equal to rlist<br>gb_epsilon_solvent = 80 ; Dielectric constant for the implicit<br>solvent<br>; gb_saltconc = 0 ; Salt concentration for implicit solvent<br>models, currently not used<br>
sa_algorithm = Ace-approximation<br>sa_surface_tension = -1<br><br><br>and for the md run:<br><br>define = -DPOSRESHELIX ; -DFLEXIBLE -DPOSRES<br>constraints = none<br>integrator = md<br>
dt = 0.001 ; ps<br>nsteps = 1000000000 ; 100000 ps = 100 ns<br>nstcomm = 10<br>nstcalcenergy = 10<br>nstxout = 1000 ; frequency to write coordinates to output<br>
trajectory<br>nstvout = 0 ; frequency to write velocities to output<br>trajectory; the last velocities are always written<br>nstfout = 0 ; frequency to write forces to output<br>trajectory<br>
nstlog = 1000 ; frequency to write energies to log<br>file<br>nstenergy = 1000 ; frequency to write energies to edr file<br><br>vdwtype = cut-off<br>coulombtype = cut-off<br>
<br>pbc = no<br><br>nstlist = 0<br>ns_type = simple<br>rlist = 0 ; this means all-vs-all (no cut-off), which<br>gets expensive for bigger systems<br>rcoulomb = 0<br>
rvdw = 0<br><br>comm-mode = angular<br>comm-grps = system<br><br>optimize_fft = yes<br><br>; V-rescale temperature coupling is on<br>Tcoupl = v-rescale<br>tau_t = 0.1<br>
tc_grps = system<br>ref_t = 300<br>; Pressure coupling is off<br>Pcoupl = no<br>; Generate velocites is on<br>gen_vel = yes<br>gen_temp = 300<br>gen_seed = -1<br>
<br>;<br>; Implicit solvent<br>;<br>implicit_solvent = GBSA<br>gb_algorithm = Still ; HCT ; OBC<br>nstgbradii = 1<br>rgbradii = 0 ; [nm] Cut-off for the calculation of the Born<br>radii. Currently must be equal to rlist<br>
gb_epsilon_solvent = 80 ; Dielectric constant for the implicit<br>solvent<br>; gb_saltconc = 0 ; Salt concentration for implicit solvent<br>models, currently not used<br>sa_algorithm = Ace-approximation<br>
sa_surface_tension = -1<br><br><br>best regards,<br>vedat<br><br><br>Am 28.02.2012 11:59, schrieb Steven Neumann:<br><br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">Dear Gmx Users,<br>I am using Gromacs 4.5.4 and I would like to implement implicit solvent<br>for folding of my protein. I read mailing list and it is still confusing for<br>
me.<br>Is it proper to use counterions within the system? If not, how can I<br>obtain netral system?<br>Do we use cut off for vdw and coulombic interactions?<br>What kind of integrator should be used with a timestep?<br>I will appreciate an mdp file for protein folding! Thank you<br>
Steven<br></blockquote>--<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a><br>
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</blockquote></blockquote><br>-- <br></div></div>==============================<u></u>==========<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>
Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" target="_blank" value="+15402319080">(540) 231-9080</a><br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>==============================<u></u>==========
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